Comments (5)
joshua-gould
commented on June 19, 2024
Please install cython first and then install wot:
pip install cython
pip install wot
…On Wed, May 22, 2019 at 11:20 AM ghoshal ***@***.***> 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_0gz_80000gn/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 <limits.h> /* 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 <limits.h> /* 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.
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from wot.
ghoshal
commented on June 19, 2024
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
from wot.
samIndeed
commented on June 19, 2024
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
^~~~~~~~~~
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/
from wot.
joshua-gould
commented on June 19, 2024
Please try installing POT with conda: conda install -c conda-forge pot
from wot.
samIndeed
commented on June 19, 2024
Oh actually I fixed it already with
conda install -c anaconda gcc
Thanks!
from wot.
Related Issues (20)
- Are all genes or highly variable genes used as input expression matrix in Waddington-OT? HOT 1
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- where to choose number of PCA to compute transport map? HOT 3
- Interpreting WOT ancestors and trajectory probabilities
- Preparation of expression matrix HOT 4
- Reading mtx file HOT 1
- What is the difference between fate probability and ancestor probability? HOT 1
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