On a new system running xubuntu 20.04, with a fresh install of conda, I get this when following our standard install instructions (curl env file followed by conda env update --file environment.yml). The only thing I did differently was to change in the environment file the line name: base to name: mne.
[... a bunch of normal output omitted...]
Building wheels for collected packages: numpydoc, mayavi
Building wheel for numpydoc (setup.py): started
Building wheel for numpydoc (setup.py): finished with status 'done'
Created wheel for numpydoc: filename=numpydoc-1.0.0.dev0-py3-none-any.whl size=47489 sha256=222954e55166d0679190b7daef71accb0ec7f525882fe36c20be228c307922f5
Stored in directory: /tmp/pip-ephem-wheel-cache-gsthnxo1/wheels/38/db/74/ae8b461756e385e9f099d8a4af23510a2c92b3001f1503ab39
Building wheel for mayavi (setup.py): started
Building wheel for mayavi (setup.py): finished with status 'error'
Running setup.py clean for mayavi
Successfully built numpydoc
Failed to build mayavi
Installing collected packages: mne, imageio-ffmpeg, vtk, scooby, appdirs, meshio, pyvista, nibabel, configobj, apptools, envisage, mayavi, PySurfer, dipy, sklearn, nilearn, quantities, neo, termcolor, pytest-sugar, snowballstemmer, pydocstyle, codespell, python-picard, tqdm, sphinxcontrib-serializinghtml, alabaster, babel, sphinxcontrib-devhelp, imagesize, sphinxcontrib-htmlhelp, urllib3, idna, chardet, requests, sphinxcontrib-jsmath, sphinxcontrib-applehelp, sphinxcontrib-qthelp, docutils, sphinx, numpydoc
Running setup.py install for mayavi: started
Running setup.py install for mayavi: finished with status 'error'
Pip subprocess error:
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/envs/mne/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-72s2xw_7/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-72s2xw_7/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 /tmp/pip-wheel-ktpbwzle
cwd: /tmp/pip-req-build-72s2xw_7/
Complete output (33 lines):
running bdist_wheel
running build
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-req-build-72s2xw_7/setup.py", line 411, in <module>
setup(
File "/opt/miniconda3/envs/mne/lib/python3.8/site-packages/numpy/distutils/core.py", line 171, in setup
return old_setup(**new_attr)
File "/opt/miniconda3/envs/mne/lib/python3.8/site-packages/setuptools/__init__.py", line 144, in setup
return distutils.core.setup(**attrs)
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/core.py", line 148, in setup
dist.run_commands()
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/opt/miniconda3/envs/mne/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 223, in run
self.run_command('build')
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-req-build-72s2xw_7/setup.py", line 268, in run
build_tvtk_classes_zip()
File "/tmp/pip-req-build-72s2xw_7/setup.py", line 254, in build_tvtk_classes_zip
gen_tvtk_classes_zip()
File "tvtk/setup.py", line 83, in gen_tvtk_classes_zip
from tvtk.code_gen import TVTKGenerator
File "/tmp/pip-req-build-72s2xw_7/tvtk/code_gen.py", line 10, in <module>
import vtk_module as vtk
File "tvtk/vtk_module.py", line 15, in <module>
from vtk import *
ModuleNotFoundError: No module named 'vtk'
----------------------------------------
ERROR: Failed building wheel for mayavi
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/envs/mne/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-72s2xw_7/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-72s2xw_7/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-jr9rwjeq/install-record.txt --single-version-externally-managed --compile --install-headers /opt/miniconda3/envs/mne/include/python3.8/mayavi
cwd: /tmp/pip-req-build-72s2xw_7/
Complete output (43 lines):
running install
running build
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-req-build-72s2xw_7/setup.py", line 411, in <module>
setup(
File "/opt/miniconda3/envs/mne/lib/python3.8/site-packages/numpy/distutils/core.py", line 171, in setup
return old_setup(**new_attr)
File "/opt/miniconda3/envs/mne/lib/python3.8/site-packages/setuptools/__init__.py", line 144, in setup
return distutils.core.setup(**attrs)
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/core.py", line 148, in setup
dist.run_commands()
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/opt/miniconda3/envs/mne/lib/python3.8/site-packages/numpy/distutils/command/install.py", line 62, in run
r = self.setuptools_run()
File "/opt/miniconda3/envs/mne/lib/python3.8/site-packages/numpy/distutils/command/install.py", line 36, in setuptools_run
return distutils_install.run(self)
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/command/install.py", line 545, in run
self.run_command('build')
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/opt/miniconda3/envs/mne/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-req-build-72s2xw_7/setup.py", line 268, in run
build_tvtk_classes_zip()
File "/tmp/pip-req-build-72s2xw_7/setup.py", line 254, in build_tvtk_classes_zip
gen_tvtk_classes_zip()
File "tvtk/setup.py", line 83, in gen_tvtk_classes_zip
from tvtk.code_gen import TVTKGenerator
File "/tmp/pip-req-build-72s2xw_7/tvtk/code_gen.py", line 10, in <module>
import vtk_module as vtk
File "tvtk/vtk_module.py", line 15, in <module>
from vtk import *
File "/opt/miniconda3/envs/mne/lib/python3.8/site-packages/vtk.py", line 30, in <module>
all_m = importlib.import_module('vtkmodules.all')
File "/opt/miniconda3/envs/mne/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/opt/miniconda3/envs/mne/lib/python3.8/site-packages/vtkmodules/all.py", line 29, in <module>
from .vtkRenderingOpenGL2 import *
ImportError: libOpenGL.so.0: cannot open shared object file: No such file or directory
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/miniconda3/envs/mne/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-72s2xw_7/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-72s2xw_7/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-jr9rwjeq/install-record.txt --single-version-externally-managed --compile --install-headers /opt/miniconda3/envs/mne/include/python3.8/mayavi Check the logs for full command output.
CondaEnvException: Pip failed
On a new system running xubuntu 20.04, with a fresh install of conda, I get this when following our standard install instructions (curl env file followed by
conda env update --file environment.yml). The only thing I did differently was to change in the environment file the linename: basetoname: mne.Summary of the problem:
ImportError: libOpenGL.so.0: cannot open shared object file: No such file or directoryRelevant part of traceback: