search

broadinstitute / wot

A software package for analyzing snapshots of developmental processes
https://broadinstitute.github.io/wot/
BSD 3-Clause "New" or "Revised" License
140 stars 34 forks source link

Installation error on MacOSX #59

Closed ghoshal closed 5 years ago

ghoshal commented 5 years ago

Hi,

I am trying to install WOT using pip on my Mac OSX but I am getting this error. I have xcode and command line tools installed already.

Collecting wot Using cached https://files.pythonhosted.org/packages/93/b0/6ff94e54ca48a2764343f04ae03bc958c8de4b97eb151427324aa96ab7b7/wot-1.0.2-py2.py3-none-any.whl Collecting POT (from wot) Using cached https://files.pythonhosted.org/packages/28/4b/7aaa1f840a359f5953dd378e0237fa8faf9b0a415ff7282b7375fbe68d27/POT-0.5.1.tar.gz Requirement already satisfied: pandas in ./anaconda3/lib/python3.7/site-packages (from wot) (0.23.4) Requirement already satisfied: scikit-learn in ./anaconda3/lib/python3.7/site-packages (from wot) (0.20.3) Requirement already satisfied: matplotlib in ./anaconda3/lib/python3.7/site-packages (from wot) (3.0.2) Requirement already satisfied: scanpy>=1.4.2 in ./anaconda3/lib/python3.7/site-packages (from wot) (1.4.3) Requirement already satisfied: scipy in ./anaconda3/lib/python3.7/site-packages (from wot) (1.1.0) Requirement already satisfied: h5py in ./anaconda3/lib/python3.7/site-packages (from wot) (2.9.0) Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from wot) (1.15.4) Requirement already satisfied: cython in ./anaconda3/lib/python3.7/site-packages (from POT->wot) (0.29.2) Requirement already satisfied: python-dateutil>=2.5.0 in ./anaconda3/lib/python3.7/site-packages (from pandas->wot) (2.7.5) Requirement already satisfied: pytz>=2011k in ./anaconda3/lib/python3.7/site-packages (from pandas->wot) (2018.7) Requirement already satisfied: cycler>=0.10 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (1.0.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (2.3.0) Requirement already satisfied: statsmodels in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.9.0) Requirement already satisfied: numba>=0.41.0 in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.43.1) Requirement already satisfied: tables in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (3.5.1) Requirement already satisfied: joblib in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.13.2) Requirement already satisfied: anndata>=0.6.15 in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.6.19) Requirement already satisfied: networkx in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (2.2) Requirement already satisfied: patsy in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.5.1) Requirement already satisfied: natsort in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (6.0.0) Requirement already satisfied: seaborn in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.9.0) Requirement already satisfied: tqdm in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (4.28.1) Requirement already satisfied: umap-learn>=0.3.0 in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.3.8) Requirement already satisfied: six in ./anaconda3/lib/python3.7/site-packages (from h5py->wot) (1.12.0) Requirement already satisfied: setuptools in ./anaconda3/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->wot) (41.0.0) Requirement already satisfied: llvmlite>=0.28.0dev0 in ./anaconda3/lib/python3.7/site-packages (from numba>=0.41.0->scanpy>=1.4.2->wot) (0.28.0) Requirement already satisfied: numexpr>=2.6.2 in ./anaconda3/lib/python3.7/site-packages (from tables->scanpy>=1.4.2->wot) (2.6.8) Requirement already satisfied: mock>=2.0 in ./anaconda3/lib/python3.7/site-packages (from tables->scanpy>=1.4.2->wot) (2.0.0) Requirement already satisfied: decorator>=4.3.0 in ./anaconda3/lib/python3.7/site-packages (from networkx->scanpy>=1.4.2->wot) (4.3.0) Requirement already satisfied: pbr>=0.11 in ./anaconda3/lib/python3.7/site-packages (from mock>=2.0->tables->scanpy>=1.4.2->wot) (5.1.3) Building wheels for collected packages: POT Building wheel for POT (setup.py) ... error ERROR: Complete output from command /Users/bibaswan/anaconda3/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/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/var/folders/lv/26lkh7m902n85b7k_m_0gz80000gn/T/pip-wheel-cpzq215 --python-tag cp37: ERROR: 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/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/bibaswan/anaconda3/include -arch x86_64 -I/Users/bibaswan/anaconda3/include -arch x86_64 -Iot/lp -I/Users/bibaswan/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/POT/ot/lp -I/Users/bibaswan/anaconda3/include/python3.7m -c ot/lp/emd_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.7/ot/lp/emd_wrap.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] In file included from /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/syslimits.h:7:0, from /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:34, from /Users/bibaswan/anaconda3/include/python3.7m/Python.h:11, from ot/lp/emd_wrap.cpp:28: /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory

include_next / recurse down to the real one /

                                                           ^

compilation terminated. 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, wot Running setup.py install for POT ... error ERROR: Complete output from command /Users/bibaswan/anaconda3/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/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/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-record-9h8k9k_e/install-record.txt --single-version-externally-managed --compile: ERROR: 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/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/bibaswan/anaconda3/include -arch x86_64 -I/Users/bibaswan/anaconda3/include -arch x86_64 -Iot/lp -I/Users/bibaswan/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/POT/ot/lp -I/Users/bibaswan/anaconda3/include/python3.7m -c ot/lp/emd_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.7/ot/lp/emd_wrap.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] In file included from /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/syslimits.h:7:0, from /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:34, from /Users/bibaswan/anaconda3/include/python3.7m/Python.h:11, from ot/lp/emd_wrap.cpp:28: /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory

include_next / recurse down to the real one /

                                                             ^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------

ERROR: Command "/Users/bibaswan/anaconda3/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/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/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-record-9h8k9k_e/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/POT/

Any help would be awesome.

joshua-gould commented 5 years ago

Please install cython first and then install wot: pip install cython pip install wot

On Wed, May 22, 2019 at 11:20 AM ghoshal notifications@github.com wrote:

Hi,

I am trying to install WOT using pip on my Mac OSX but I am getting this error. I have xcode and command line tools installed already. Collecting wot Using cached https://files.pythonhosted.org/packages/93/b0/6ff94e54ca48a2764343f04ae03bc958c8de4b97eb151427324aa96ab7b7/wot-1.0.2-py2.py3-none-any.whl Collecting POT (from wot) Using cached https://files.pythonhosted.org/packages/28/4b/7aaa1f840a359f5953dd378e0237fa8faf9b0a415ff7282b7375fbe68d27/POT-0.5.1.tar.gz Requirement already satisfied: pandas in ./anaconda3/lib/python3.7/site-packages (from wot) (0.23.4) Requirement already satisfied: scikit-learn in ./anaconda3/lib/python3.7/site-packages (from wot) (0.20.3) Requirement already satisfied: matplotlib in ./anaconda3/lib/python3.7/site-packages (from wot) (3.0.2) Requirement already satisfied: scanpy>=1.4.2 in ./anaconda3/lib/python3.7/site-packages (from wot) (1.4.3) Requirement already satisfied: scipy in ./anaconda3/lib/python3.7/site-packages (from wot) (1.1.0) Requirement already satisfied: h5py in ./anaconda3/lib/python3.7/site-packages (from wot) (2.9.0) Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from wot) (1.15.4) Requirement already satisfied: cython in ./anaconda3/lib/python3.7/site-packages (from POT->wot) (0.29.2) Requirement already satisfied: python-dateutil>=2.5.0 in ./anaconda3/lib/python3.7/site-packages (from pandas->wot) (2.7.5) Requirement already satisfied: pytz>=2011k in ./anaconda3/lib/python3.7/site-packages (from pandas->wot) (2018.7) Requirement already satisfied: cycler>=0.10 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (1.0.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (2.3.0) Requirement already satisfied: statsmodels in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.9.0) Requirement already satisfied: numba>=0.41.0 in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.43.1) Requirement already satisfied: tables in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (3.5.1) Requirement already satisfied: joblib in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.13.2) Requirement already satisfied: anndata>=0.6.15 in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.6.19) Requirement already satisfied: networkx in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (2.2) Requirement already satisfied: patsy in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.5.1) Requirement already satisfied: natsort in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (6.0.0) Requirement already satisfied: seaborn in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.9.0) Requirement already satisfied: tqdm in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (4.28.1) Requirement already satisfied: umap-learn>=0.3.0 in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.3.8) Requirement already satisfied: six in ./anaconda3/lib/python3.7/site-packages (from h5py->wot) (1.12.0) Requirement already satisfied: setuptools in ./anaconda3/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->wot) (41.0.0) Requirement already satisfied: llvmlite>=0.28.0dev0 in ./anaconda3/lib/python3.7/site-packages (from numba>=0.41.0->scanpy>=1.4.2->wot) (0.28.0) Requirement already satisfied: numexpr>=2.6.2 in ./anaconda3/lib/python3.7/site-packages (from tables->scanpy>=1.4.2->wot) (2.6.8) Requirement already satisfied: mock>=2.0 in ./anaconda3/lib/python3.7/site-packages (from tables->scanpy>=1.4.2->wot) (2.0.0) Requirement already satisfied: decorator>=4.3.0 in ./anaconda3/lib/python3.7/site-packages (from networkx->scanpy>=1.4.2->wot) (4.3.0) Requirement already satisfied: pbr>=0.11 in ./anaconda3/lib/python3.7/site-packages (from mock>=2.0->tables->scanpy>=1.4.2->wot) (5.1.3) Building wheels for collected packages: POT Building wheel for POT (setup.py) ... error ERROR: Complete output from command /Users/bibaswan/anaconda3/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/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/var/folders/lv/26lkh7m902n85b7k_m_0gz80000gn/T/pip-wheel-cpzq215 --python-tag cp37: ERROR: 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/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/bibaswan/anaconda3/include -arch x86_64 -I/Users/bibaswan/anaconda3/include -arch x86_64 -Iot/lp -I/Users/bibaswan/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/POT/ot/lp -I/Users/bibaswan/anaconda3/include/python3.7m -c ot/lp/emd_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.7/ot/lp/emd_wrap.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] In file included from /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/syslimits.h:7:0, from /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:34, from /Users/bibaswan/anaconda3/include/python3.7m/Python.h:11, from ot/lp/emd_wrap.cpp:28: /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory

include_next / recurse down to the real one /

^ compilation terminated. 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, wot Running setup.py install for POT ... error ERROR: Complete output from command /Users/bibaswan/anaconda3/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/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/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-record-9h8k9k_e/install-record.txt --single-version-externally-managed --compile: ERROR: 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/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/bibaswan/anaconda3/include -arch x86_64 -I/Users/bibaswan/anaconda3/include -arch x86_64 -Iot/lp -I/Users/bibaswan/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/POT/ot/lp -I/Users/bibaswan/anaconda3/include/python3.7m -c ot/lp/emd_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.7/ot/lp/emd_wrap.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] In file included from /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/syslimits.h:7:0, from /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:34, from /Users/bibaswan/anaconda3/include/python3.7m/Python.h:11, from ot/lp/emd_wrap.cpp:28: /Users/bibaswan/anaconda3/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory

include_next / recurse down to the real one /

^ compilation terminated. error: command 'gcc' failed with exit status 1

ERROR: Command "/Users/bibaswan/anaconda3/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/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/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-record-9h8k9k_e/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/lv/26lkh7m902n85b7k_m_0gz_80000gn/T/pip-install-6zgo6l_s/POT/

Any help would be awesome.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/wot/issues/59?email_source=notifications&email_token=ABH6TH6JPXIBKCHIU3UBHT3PWVQCBA5CNFSM4HOVNOB2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GVHW65Q, or mute the thread https://github.com/notifications/unsubscribe-auth/ABH6TH4YLTTNKQ4DVAR4YFDPWVQCBANCNFSM4HOVNOBQ .

ghoshal commented 5 years ago

Hi,

The problem was happening in the command line tools. Needed to go to /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg location and install package manually. That solved the problem.

P.S. I had cython installed already.

Thanks

samIndeed commented 5 years ago

Hi,

I'm getting the same error and I have cython installed and manually installing those headers didn't work

Actually not quite the same error. Here is mine

pip install wot Collecting wot Using cached https://files.pythonhosted.org/packages/cc/6e/695eb40ec170d18679edfed1a12b6d00eb17dce3bace720c62cf6d38db36/wot-1.0.5-py2.py3-none-any.whl Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from wot) (1.16.2) Requirement already satisfied: matplotlib in ./anaconda3/lib/python3.7/site-packages (from wot) (3.0.3) Requirement already satisfied: pandas in ./anaconda3/lib/python3.7/site-packages (from wot) (0.24.2) Requirement already satisfied: scanpy>=1.4.2 in ./anaconda3/lib/python3.7/site-packages (from wot) (1.4.3) Collecting POT (from wot) Using cached https://files.pythonhosted.org/packages/28/4b/7aaa1f840a359f5953dd378e0237fa8faf9b0a415ff7282b7375fbe68d27/POT-0.5.1.tar.gz Requirement already satisfied: scipy in ./anaconda3/lib/python3.7/site-packages (from wot) (1.2.1) Requirement already satisfied: scikit-learn in ./anaconda3/lib/python3.7/site-packages (from wot) (0.20.3) Requirement already satisfied: h5py in ./anaconda3/lib/python3.7/site-packages (from wot) (2.9.0) Requirement already satisfied: cycler>=0.10 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (1.0.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (2.3.1) Requirement already satisfied: python-dateutil>=2.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib->wot) (2.8.0) Requirement already satisfied: pytz>=2011k in ./anaconda3/lib/python3.7/site-packages (from pandas->wot) (2018.9) Requirement already satisfied: patsy in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.5.1) Requirement already satisfied: natsort in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (6.0.0) Requirement already satisfied: joblib in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.13.2) Requirement already satisfied: seaborn in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.9.0) Requirement already satisfied: numba>=0.41.0 in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.43.1) Requirement already satisfied: anndata>=0.6.15 in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.6.22.post1) Requirement already satisfied: tqdm in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (4.31.1) Requirement already satisfied: statsmodels in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.9.0) Requirement already satisfied: tables in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (3.5.1) Requirement already satisfied: umap-learn>=0.3.0 in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (0.3.9) Requirement already satisfied: networkx in ./anaconda3/lib/python3.7/site-packages (from scanpy>=1.4.2->wot) (2.2) Requirement already satisfied: cython in ./anaconda3/lib/python3.7/site-packages (from POT->wot) (0.29.6) Requirement already satisfied: six in ./anaconda3/lib/python3.7/site-packages (from h5py->wot) (1.12.0) Requirement already satisfied: setuptools in ./anaconda3/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->wot) (40.8.0) Requirement already satisfied: llvmlite>=0.28.0dev0 in ./anaconda3/lib/python3.7/site-packages (from numba>=0.41.0->scanpy>=1.4.2->wot) (0.28.0) Requirement already satisfied: numexpr>=2.6.2 in ./anaconda3/lib/python3.7/site-packages (from tables->scanpy>=1.4.2->wot) (2.6.9) Collecting mock>=2.0 (from tables->scanpy>=1.4.2->wot) Using cached https://files.pythonhosted.org/packages/05/d2/f94e68be6b17f46d2c353564da56e6fb89ef09faeeff3313a046cb810ca9/mock-3.0.5-py2.py3-none-any.whl Requirement already satisfied: decorator>=4.3.0 in ./anaconda3/lib/python3.7/site-packages (from networkx->scanpy>=1.4.2->wot) (4.4.0) Building wheels for collected packages: POT Building wheel for POT (setup.py) ... error Complete output from command /Users/sampalmer/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/sl/n9mc8fp163j6cz0h7f3pwb_h0000gn/T/pip-install-tqt04974/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/var/folders/sl/n9mc8fp163j6cz0h7f3pwb_h0000gn/T/pip-wheel-wko8p8ir --python-tag cp37: 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/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/sampalmer/anaconda3/include -arch x86_64 -I/Users/sampalmer/anaconda3/include -arch x86_64 -Iot/lp -I/Users/sampalmer/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/private/var/folders/sl/n9mc8fp163j6cz0h7f3pwb_h0000gn/T/pip-install-tqt04974/POT/ot/lp -I/Users/sampalmer/anaconda3/include/python3.7m -c ot/lp/emd_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.7/ot/lp/emd_wrap.o 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 ot/lp/emd_wrap.cpp:631: In file included from /Users/sampalmer/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Users/sampalmer/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/sampalmer/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824: /Users/sampalmer/anaconda3/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:633: 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

Failed building wheel for POT Running setup.py clean for POT Failed to build POT Installing collected packages: POT, wot, mock Running setup.py install for POT ... error Complete output from command /Users/sampalmer/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/sl/n9mc8fp163j6cz0h7f3pwb_h0000gn/T/pip-install-tqt04974/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/var/folders/sl/n9mc8fp163j6cz0h7f3pwb_h0000gn/T/pip-record-hxxga7yx/install-record.txt --single-version-externally-managed --compile: 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/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/sampalmer/anaconda3/include -arch x86_64 -I/Users/sampalmer/anaconda3/include -arch x86_64 -Iot/lp -I/Users/sampalmer/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/private/var/folders/sl/n9mc8fp163j6cz0h7f3pwb_h0000gn/T/pip-install-tqt04974/POT/ot/lp -I/Users/sampalmer/anaconda3/include/python3.7m -c ot/lp/emd_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.7/ot/lp/emd_wrap.o 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 ot/lp/emd_wrap.cpp:631: In file included from /Users/sampalmer/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Users/sampalmer/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/sampalmer/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824: /Users/sampalmer/anaconda3/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:633:
ot/lp/EMD.h:19:10: fatal error: 'iostream' file not found
#include <iostream>
         ^~~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1

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

Command "/Users/sampalmer/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/sl/n9mc8fp163j6cz0h7f3pwb_h0000gn/T/pip-install-tqt04974/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/var/folders/sl/n9mc8fp163j6cz0h7f3pwb_h0000gn/T/pip-record-hxxga7yx/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/sl/n9mc8fp163j6cz0h7f3pwb_h0000gn/T/pip-install-tqt04974/POT/

joshua-gould commented 5 years ago

Please try installing POT with conda: conda install -c conda-forge pot

samIndeed commented 5 years ago

Oh actually I fixed it already with

conda install -c anaconda gcc

Thanks!