install is broken for me
bendichter opened this issue · comments
(base) Bens-MacBook-Pro-2:dev bendichter$ conda env create -f img_pipe/environment_py35.yml
Collecting package metadata: done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Ran pip subprocess with arguments:
['/anaconda3/envs/img_pipe_py3/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt']
Pip subprocess output:
Collecting configparser==3.5.0 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 1))
Collecting cycler==0.10.0 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 2))
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting img-pipe==2017.8.19.3 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Using cached https://files.pythonhosted.org/packages/da/78/9e3f265453eafc6daca990299ceb456d2dcc4475963ed2eab89b1a45fd74/img_pipe-2017.8.19.3-py3-none-any.whl
Requirement already up-to-date: ipython-genutils==0.2.0 in /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 4))
Collecting matplotlib==1.5.3 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/79/a7/c7409e39e164ece35f23e02b43b069a3eb8453726b26f59cd391b7736955/matplotlib-1.5.3-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting mne==0.14.1 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 6))
Collecting mpmath==0.19 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 7))
Collecting nibabel==2.1.0 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 8))
Collecting nipy==0.4.1 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 9))
Using cached https://files.pythonhosted.org/packages/38/77/b7a665f098bbfc1e8f1564e7e53029aa0d0cc271d7661ab3fc0cdece3603/nipy-0.4.1-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already up-to-date: prompt-toolkit==1.0.14 in /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 10))
Collecting pymcubes==0.0.6 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 11))
Using cached https://files.pythonhosted.org/packages/26/10/16b78657eb3fcd49a6908e9bbe2ff8069805ce7823f31ea945213ca0ca06/PyMCubes-0.0.6.tar.gz
Collecting pyparsing==2.2.0 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 12))
Using cached https://files.pythonhosted.org/packages/6a/8a/718fd7d3458f9fab8e67186b00abdd345b639976bc7fb3ae722e1b026a50/pyparsing-2.2.0-py2.py3-none-any.whl
Collecting python-dateutil==2.6.1 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 13))
Using cached https://files.pythonhosted.org/packages/4b/0d/7ed381ab4fe80b8ebf34411d14f253e1cf3e56e2820ffa1d8844b23859a2/python_dateutil-2.6.1-py2.py3-none-any.whl
Collecting pytz==2017.2 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 14))
Using cached https://files.pythonhosted.org/packages/55/62/e7cd0e15b76062d298413f14bb4ec3cd8568a22d274427f9c3c7286969f4/pytz-2017.2-py2.py3-none-any.whl
Collecting pyvtk==0.5.18 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 15))
Collecting sympy==1.1.1 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 16))
Collecting tqdm==4.15.0 (from -r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 17))
Using cached https://files.pythonhosted.org/packages/4b/8c/f578581f1ea3e65af88a0c30c3d09d264b01acf585c1e6dcde022fbc664b/tqdm-4.15.0-py2.py3-none-any.whl
Collecting six (from cycler==0.10.0->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 2))
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting scipy (from img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Using cached https://files.pythonhosted.org/packages/94/7e/6e0ec6fa5b063fc7324beed41c246037813b7577b36dff7ea6ff8fa15d55/scipy-1.2.1-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting mayavi (from img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Collecting numpy (from img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Using cached https://files.pythonhosted.org/packages/5a/ea/f524e88a6f9090caa633fc76f61c3cb28d9c1814be9a440750916e4d7dc3/numpy-1.16.3-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already up-to-date: wcwidth in /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages (from prompt-toolkit==1.0.14->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 10))
Collecting pygments (from mayavi->img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Using cached https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl
Collecting pyface>=6.0.0 (from mayavi->img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Collecting envisage (from mayavi->img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Collecting traits>=4.6.0 (from mayavi->img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Collecting vtk (from mayavi->img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Using cached https://files.pythonhosted.org/packages/8b/b6/0a4d3da43732cbf4fb5dfa180962439d1f7431e4e38446c22fc22365e040/vtk-8.1.2-cp35-cp35m-macosx_10_6_x86_64.whl
Collecting traitsui>=6.0.0 (from mayavi->img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Requirement already up-to-date: apptools in /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages (from mayavi->img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Requirement already up-to-date: configobj in /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages (from apptools->mayavi->img-pipe==2017.8.19.3->-r /Users/bendichter/dev/img_pipe/condaenv.pzlbewc1.requirements.txt (line 3))
Building wheels for collected packages: pymcubes
Running setup.py bdist_wheel for pymcubes: started
Running setup.py bdist_wheel for pymcubes: finished with status 'error'
Complete output from command /anaconda3/envs/img_pipe_py3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/mc/k9f_f9bn6h11j5t97_12s2jc0000gn/T/pip-build-l24pq46a/pymcubes/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 /var/folders/mc/k9f_f9bn6h11j5t97_12s2jc0000gn/T/tmpwdn660mhpip-wheel- --python-tag cp35:
Warning: Extension name 'mcubes._mcubes' does not match fully qualified name '_mcubes' of 'mcubes/src/_mcubes.pyx'
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.5
creating build/lib.macosx-10.7-x86_64-3.5/mcubes
copying mcubes/exporter.py -> build/lib.macosx-10.7-x86_64-3.5/mcubes
copying mcubes/__init__.py -> build/lib.macosx-10.7-x86_64-3.5/mcubes
running build_ext
building 'mcubes._mcubes' extension
creating build/temp.macosx-10.7-x86_64-3.5
creating build/temp.macosx-10.7-x86_64-3.5/mcubes
creating build/temp.macosx-10.7-x86_64-3.5/mcubes/src
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/envs/img_pipe_py3/include -arch x86_64 -Imcubes/src -I/anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages/numpy/core/include -I/anaconda3/envs/img_pipe_py3/include/python3.5m -c mcubes/src/_mcubes.cpp -o build/temp.macosx-10.7-x86_64-3.5/mcubes/src/_mcubes.o -std=c++11
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 mcubes/src/_mcubes.cpp:528:
In file included from /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:
/anaconda3/envs/img_pipe_py3/lib/python3.5/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 " \
^
In file included from mcubes/src/_mcubes.cpp:530:
In file included from mcubes/src/pywrapper.h:6:
mcubes/src/pyarraymodule.h:6:10: fatal error: 'stdexcept' file not found
#include <stdexcept>
^~~~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Running setup.py clean for pymcubes
Failed to build pymcubes
Installing collected packages: configparser, six, cycler, pyvtk, numpy, scipy, pymcubes, nibabel, mpmath, sympy, nipy, tqdm, pygments, traits, pyface, envisage, vtk, traitsui, mayavi, mne, python-dateutil, pytz, pyparsing, matplotlib, img-pipe
Found existing installation: six 1.10.0
Uninstalling six-1.10.0:
Successfully uninstalled six-1.10.0
Found existing installation: numpy 1.13.1
Uninstalling numpy-1.13.1:
Successfully uninstalled numpy-1.13.1
Found existing installation: scipy 0.19.1
Uninstalling scipy-0.19.1:
Successfully uninstalled scipy-0.19.1
Running setup.py install for pymcubes: started
Running setup.py install for pymcubes: finished with status 'error'
Complete output from command /anaconda3/envs/img_pipe_py3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/mc/k9f_f9bn6h11j5t97_12s2jc0000gn/T/pip-build-l24pq46a/pymcubes/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/mc/k9f_f9bn6h11j5t97_12s2jc0000gn/T/pip-8ce7fvbb-record/install-record.txt --single-version-externally-managed --compile:
Warning: Extension name 'mcubes._mcubes' does not match fully qualified name '_mcubes' of 'mcubes/src/_mcubes.pyx'
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.5
creating build/lib.macosx-10.7-x86_64-3.5/mcubes
copying mcubes/exporter.py -> build/lib.macosx-10.7-x86_64-3.5/mcubes
copying mcubes/__init__.py -> build/lib.macosx-10.7-x86_64-3.5/mcubes
running build_ext
building 'mcubes._mcubes' extension
creating build/temp.macosx-10.7-x86_64-3.5
creating build/temp.macosx-10.7-x86_64-3.5/mcubes
creating build/temp.macosx-10.7-x86_64-3.5/mcubes/src
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/envs/img_pipe_py3/include -arch x86_64 -Imcubes/src -I/anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages/numpy/core/include -I/anaconda3/envs/img_pipe_py3/include/python3.5m -c mcubes/src/_mcubes.cpp -o build/temp.macosx-10.7-x86_64-3.5/mcubes/src/_mcubes.o -std=c++11
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 mcubes/src/_mcubes.cpp:528:
In file included from /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/img_pipe_py3/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/anaconda3/envs/img_pipe_py3/lib/python3.5/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 mcubes/src/_mcubes.cpp:530:
In file included from mcubes/src/pywrapper.h:6:
mcubes/src/pyarraymodule.h:6:10: fatal error: 'stdexcept' file not found
#include <stdexcept>
^~~~~~~~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Pip subprocess error:
Failed building wheel for pymcubes
DEPRECATION: Uninstalling a distutils installed project (six) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
Command "/anaconda3/envs/img_pipe_py3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/mc/k9f_f9bn6h11j5t97_12s2jc0000gn/T/pip-build-l24pq46a/pymcubes/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/mc/k9f_f9bn6h11j5t97_12s2jc0000gn/T/pip-8ce7fvbb-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/mc/k9f_f9bn6h11j5t97_12s2jc0000gn/T/pip-build-l24pq46a/pymcubes/
You are using pip version 9.0.1, however version 19.0.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
CondaEnvException: Pip failed
Upgrade your pip and try again.
I experienced a similar issue (upgrading pip did not work) however this is what did work for me:
export MACOSX_DEPLOYMENT_TARGET=10.10
CFLAGS=-stdlib=libc++ pip install pymcubes
thanks to this thread!
Note, I am running macOS 10.15.5 Catalina