VTK Module Import Error | Anaconda Windows 10

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Dear mne-community,

first of all, thanks a lot for your great work on mne-python, I am
benefiting a lot from it.
I read the issue about vtk and pip, probably my problem is related to this
issue (BUG: environment.yml not working on Appveyor · Issue #5858 · mne-tools/mne-python · GitHub).

This weekend, I tried to install mne-python according to your instructions
and got this *ModuleNotFoundError* when the wheel for mayavi was built:

*Building wheels for collected packages: mayavi Running setup.py
bdist_wheel for mayavi ... error Complete output from command
C:\Anaconda3\envs\mne\python.exe -u -c "import setuptools,
tokenize;__file__='C:\\Users\\RCHNER~1\\AppData\\Local\\Temp\\pip-req-build-b24h2ill\\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
C:\Users\RCHNER~1\AppData\Local\Temp\pip-wheel-q3jzjwws --python-tag cp36:
running bdist_wheel running build Traceback (most recent call last):
File "C:\Anaconda3\envs\mne\lib\site-packages\vtk\vtkIOImage.py", line 5,
in <module> from .vtkIOImagePython import * ImportError: DLL load
failed: Das angegebene Modul wurde nicht gefunden. During handling of the
above exception, another exception occurred: Traceback (most recent call
last): File "<string>", line 1, in <module> File
"C:\Users\RCHNER~1\AppData\Local\Temp\pip-req-build-b24h2ill\setup.py",
line 470, in <module> **config File
"C:\Anaconda3\envs\mne\lib\site-packages\numpy\distutils\core.py", line
169, in setup return old_setup(**new_attr) File
"C:\Anaconda3\envs\mne\lib\site-packages\setuptools\__init__.py", line 143,
in setup return distutils.core.setup(**attrs) File
"C:\Anaconda3\envs\mne\lib\distutils\core.py", line 148, in setup
dist.run_commands() File "C:\Anaconda3\envs\mne\lib\distutils\dist.py",
line 955, in run_commands self.run_command(cmd) File
"C:\Anaconda3\envs\mne\lib\distutils\dist.py", line 974, in
run_command cmd_obj.run() File
"C:\Anaconda3\envs\mne\lib\site-packages\wheel\bdist_wheel.py", line 188,
in run self.run_command('build') File
"C:\Anaconda3\envs\mne\lib\distutils\cmd.py", line 313, in run_command
self.distribution.run_command(command) File
"C:\Anaconda3\envs\mne\lib\distutils\dist.py", line 974, in
run_command cmd_obj.run() File
"C:\Users\RCHNER~1\AppData\Local\Temp\pip-req-build-b24h2ill\setup.py",
line 268, in run build_tvtk_classes_zip() File
"C:\Users\RCHNER~1\AppData\Local\Temp\pip-req-build-b24h2ill\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
"C:\Users\RCHNER~1\AppData\Local\Temp\pip-req-build-b24h2ill\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
"C:\Anaconda3\envs\mne\lib\site-packages\vtk\__init__.py", line 56, in
<module> from .vtkIOImage import * File
"C:\Anaconda3\envs\mne\lib\site-packages\vtk\vtkIOImage.py", line 9, in
<module> from vtkIOImagePython import * ModuleNotFoundError: No
module named 'vtkIOImagePython'*

I tried the same on another windows computer, and got the same error. The
installation on Ubuntu is working.
After *changing the channel in environment.yml to conda-forge*, the
environment and mayavi could be installed. But the versions of several
packages are lower than in the channel=default installation.
Those are the outputs of mne.sys_info() from the failed and the
conda-forge-environment:

Python 3.6.8 |Anaconda, Inc.| (default, Dec 30 2018, 18:50:55) [MSC v.1915
64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.

import mne
mne.sys_info()

Platform: Windows-10-10.0.17763-SP0
Python: 3.6.8 |Anaconda, Inc.| (default, Dec 30 2018, 18:50:55) [MSC
v.1915 64 bit (AMD64)]
Executable: C:\Anaconda3\envs\mne\python.exe
CPU: Intel64 Family 6 Model 158 Stepping 9, GenuineIntel: 8 cores
Memory: 15.9 GB

mne: 0.17.0
numpy: 1.15.4 {blas=mkl_rt, lapack=mkl_rt}
scipy: 1.2.0
matplotlib: 3.0.2 {backend=Qt5Agg}

sklearn: 0.20.2
nibabel: 2.3.3
mayavi: Not found
cupy: Not found
pandas: 0.24.0
dipy: Not found

Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 11:48:23)
[MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.

import mne
mne.sys_info()

C:\Anaconda3\envs\mne_cf\lib\site-packages\sklearn\externals\joblib\externals\cloudpickle\cloudpickle.py:47:
DeprecationWarning: the imp module is deprecated in favour of importlib;
see the module's documentation for alternative uses
  import imp
Platform: Windows-10-10.0.17763-SP0
Python: 3.6.6 | packaged by conda-forge | (default, Jul 26 2018,
11:48:23) [MSC v.1900 64 bit (AMD64)]
Executable: C:\Anaconda3\envs\mne_cf\python.exe
CPU: Intel64 Family 6 Model 158 Stepping 9, GenuineIntel: 8 cores
Memory: 15.9 GB

mne: 0.17.0
numpy: 1.15.4 {blas=mkl_rt, lapack=mkl_rt}
scipy: 1.1.0
matplotlib: 3.0.0 {backend=Qt5Agg}

sklearn: 0.20.0
nibabel: 2.3.3
mayavi: 4.7.0.dev0 {qt_api=pyqt5, PyQt5=5.9.2}
cupy: Not found
pandas: 0.24.0
dipy: 0.13.0

I am a very beginner in conda and python and can't really understand the
problem. Is mne-python also working with the conda-forge-packages?

Kind regards,
Martin
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hi Martin,

we have since a few days issues with windows packaging.
It may be due to the new updates to conda-forge.

did you try to change the environment.yml file in any way?
did you just change the channel globally on your conda install?

Alex

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Hi Alex,

thank you for the quick answer.
I changed the channel parameter in the environment.yml from defaults to
conda-forge. I did not change anything in .condarc. It was only a try,
because I read something about conda-forge in this discussion:
https://github.com/conda-forge/vtk-feedstock/issues/21

And i was surprised and happy, that it worked so I could continue analyzing.
I haven't encountered any unusual errors yet, Mayavi works. But maybe, it
is a problem and I only wanted to ask, if there is an easy solution to this
problem, because it would be easier to install mne following your
instructions.
Thank you.

Martin

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hi,

we would need to be able to replicate. Currently appveyor we use for
testing on windows is green :
https://ci.appveyor.com/project/mne-tools/mne-python/branch/master

not sure how we can replicate the problem then.

Alex

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We saw this problem crop up a week or two ago, and just did a quick
workaround
<https://github.com/mne-tools/mne-python/pull/5845/files#diff-180360612c6b8c4ed830919bbb4dd459R7>
that involves manually running a `conda install` and then `pip` install.
There seems to be an upstream bug with VTK that we are hoping to track down
<https://github.com/mne-tools/mne-python/pull/5845#issuecomment-456929811>
to avoid needing to do this.

Eric

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Hi Eric and Alex,

I got no experience with the usage of appveyor.
But I can report, that I just tried to reinstall mne with the current
environment.yml file from the website and it finally seemed to work with
the pip-workaround.
There still was an error, when building the mayavi wheel.
But when vtk was intalled via pip, mayavi was apparently also installed.

Another thing I saw ist, that when I would try conda install cupy, python
and many other package are downgraded again to their 3.6 version (you had
declared it to 3.7 now).

Thank you for the ongoing developement
Martin

*(base) C:\Users\R?chner>conda env create -f environment_2.ymlCollecting
package metadata: doneSolving environment: donePreparing transaction:
doneVerifying transaction: doneExecuting transaction: | DEBUG
menuinst_win32:__init__(196): Menu: name: 'Anaconda${PY_VER} \{PLATFORM\}&#39;, prefix: &#39;C:\\Anaconda3\\envs\\mne\_2&#39;, env\_name: &#39;mne\_2&#39;, mode: &#39;user&#39;, used\_mode: &#39;user&#39;DEBUG menuinst\_win32:create\(320\): Shortcut cmd is C:\\Anaconda3\\python\.exe, args are \[&#39;C:\\\\Anaconda3\\\\cwp\.py&#39;, &#39;C:\\\\Anaconda3\\\\envs\\\\mne\_2&#39;, &#39;C:\\\\Anaconda3\\\\envs\\\\mne\_2\\\\python\.exe&#39;, &#39;C:\\\\Anaconda3\\\\envs\\\\mne\_2\\\\Scripts\\\\jupyter\-notebook\-script\.py&#39;, &#39;&quot;%USERPROFILE%/&quot;&#39;\]/ DEBUG menuinst\_win32:\_\_init\_\_\(196\): Menu: name: &#39;Anaconda{PY_VER} ${PLATFORM}', prefix: 'C:\Anaconda3\envs\mne_2',
env_name: 'mne_2', mode: 'user', used_mode: 'user'DEBUG
menuinst_win32:create(320): Shortcut cmd is C:\Anaconda3\pythonw.exe, args
are ['C:\\Anaconda3\\cwp.py', 'C:\\Anaconda3\\envs\\mne_2',
'C:\\Anaconda3\\envs\\mne_2\\pythonw.exe',
'C:\\Anaconda3\\envs\\mne_2\\Scripts\\spyder-script.py']DEBUG
menuinst_win32:create(320): Shortcut cmd is C:\Anaconda3\python.exe, args
are ['C:\\Anaconda3\\cwp.py', 'C:\\Anaconda3\\envs\\mne_2',
'C:\\Anaconda3\\envs\\mne_2\\python.exe',
'C:\\Anaconda3\\envs\\mne_2\\Scripts\\spyder-script.py',
'--reset']doneCollecting
https://api.github.com/repos/enthought/mayavi/zipball/226189a6ad3dc3c01d031ef21d0d0cde554ac851
<https://api.github.com/repos/enthought/mayavi/zipball/226189a6ad3dc3c01d031ef21d0d0cde554ac851&gt;
(from -r C:\Users\R?chner\condaenv.4puw230_.requirements.txt (line 3))
Downloading
https://api.github.com/repos/enthought/mayavi/zipball/226189a6ad3dc3c01d031ef21d0d0cde554ac851
<https://api.github.com/repos/enthought/mayavi/zipball/226189a6ad3dc3c01d031ef21d0d0cde554ac851&gt;
/ 20.8MB 6.6MB/sCollecting mne (from -r
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Using cached
https://files.pythonhosted.org/packages/6b/55/e4f0cdf6634def017a98374a6930ffdd65d84b8ddf1c885a08728de5b408/vtk-8.1.2-cp37-cp37m-win_amd64.whl
<https://files.pythonhosted.org/packages/6b/55/e4f0cdf6634def017a98374a6930ffdd65d84b8ddf1c885a08728de5b408/vtk-8.1.2-cp37-cp37m-win_amd64.whl&gt;Collecting
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dipy (from -r C:\Users\R?chner\condaenv.4puw230_.requirements.txt (line
5)) Using cached
https://files.pythonhosted.org/packages/ac/90/7fbb0db04cefa8711f8ea4d6b853428ef380b7b701b8b9320135a37a80c1/dipy-0.15.0-cp37-none-win_amd64.whl
<https://files.pythonhosted.org/packages/ac/90/7fbb0db04cefa8711f8ea4d6b853428ef380b7b701b8b9320135a37a80c1/dipy-0.15.0-cp37-none-win_amd64.whl&gt;Collecting
nibabel (from -r C:\Users\R?chner\condaenv.4puw230_.requirements.txt (line
6)) Using cached
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<https://files.pythonhosted.org/packages/0a/36/a9e7ef516d0f63c2610c0033daf06c1001b1b70943f08c89d502c19bedf6/nibabel-2.3.3-py3-none-any.whl&gt;Collecting
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<https://files.pythonhosted.org/packages/3d/9e/96f2da387ee9acaba2cbab7b596486b0231b5f6d9bf946b880536d4485fc/nilearn-0.5.0-py2.py3-none-any.whl&gt;Collecting
neo (from -r C:\Users\R?chner\condaenv.4puw230_.requirements.txt (line
8))Collecting pytest-faulthandler (from -r
C:\Users\R?chner\condaenv.4puw230_.requirements.txt (line 9)) Using cached
https://files.pythonhosted.org/packages/52/d7/13e81ff8f3f9e2ee3d22a59e0d09a4010aaa21b41dd088d757148ccca2be/pytest_faulthandler-1.5.0-py2.py3-none-any.whl
<https://files.pythonhosted.org/packages/52/d7/13e81ff8f3f9e2ee3d22a59e0d09a4010aaa21b41dd088d757148ccca2be/pytest_faulthandler-1.5.0-py2.py3-none-any.whl&gt;Collecting
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(line 10)) Using cached
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<https://files.pythonhosted.org/packages/6e/3f/9207e1af3fb23c71a2a17a5d82d4c68f4dd6b3429b58514c74b95f6e0784/pydocstyle-3.0.0-py3-none-any.whl&gt;Collecting
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already satisfied: numpy in c:\anaconda3\envs\mne_2\lib\site-packages (from
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(3.0.2)Collecting imageio>=1.5; extra == "save_movie" (from
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(0.4.1)Building wheels for collected packages: mayavi Running setup.py
bdist_wheel for mayavi ... error Complete output from command
C:\Anaconda3\envs\mne_2\python.exe -u -c "import setuptools,
tokenize;__file__='C:\\Users\\RCHNER~1\\AppData\\Local\\Temp\\pip-req-build-z4qlrqgb\\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
C:\Users\RCHNER~1\AppData\Local\Temp\pip-wheel-i4aodd4g --python-tag cp37:
running bdist_wheel running build Traceback (most recent call last):
File "<string>", line 1, in <module> File
"C:\Users\RCHNER~1\AppData\Local\Temp\pip-req-build-z4qlrqgb\setup.py",
line 474, in <module> **config File
"C:\Anaconda3\envs\mne_2\lib\site-packages\numpy\distutils\core.py", line
169, in setup return old_setup(**new_attr) File
"C:\Anaconda3\envs\mne_2\lib\site-packages\setuptools\__init__.py", line
143, in setup return distutils.core.setup(**attrs) File
"C:\Anaconda3\envs\mne_2\lib\distutils\core.py", line 148, in setup
dist.run_commands() File
"C:\Anaconda3\envs\mne_2\lib\distutils\dist.py", line 966, in
run_commands self.run_command(cmd) File
"C:\Anaconda3\envs\mne_2\lib\distutils\dist.py", line 985, in
run_command cmd_obj.run() File
"C:\Anaconda3\envs\mne_2\lib\site-packages\wheel\bdist_wheel.py", line 188,
in run self.run_command('build') File
"C:\Anaconda3\envs\mne_2\lib\distutils\cmd.py", line 313, in
run_command self.distribution.run_command(command) File
"C:\Anaconda3\envs\mne_2\lib\distutils\dist.py", line 985, in
run_command cmd_obj.run() File
"C:\Users\RCHNER~1\AppData\Local\Temp\pip-req-build-z4qlrqgb\setup.py",
line 268, in run build_tvtk_classes_zip() File
"C:\Users\RCHNER~1\AppData\Local\Temp\pip-req-build-z4qlrqgb\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
"C:\Users\RCHNER~1\AppData\Local\Temp\pip-req-build-z4qlrqgb\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'
---------------------------------------- Failed building wheel for mayavi
Running setup.py clean for mayaviFailed to build mayaviInstalling collected
packages: mne, vtk, configobj, apptools, envisage, mayavi, bz2file,
nibabel, imageio, PySurfer, dipy, nilearn, quantities, neo,
pytest-faulthandler, pydocstyle, codespell, python-picard Running setup.py
install for mayavi ... done The scripts imageio_download_bin.exe and
imageio_remove_bin.exe are installed in 'C:\Anaconda3\envs\mne_2\Scripts'
which is not on PATH. Consider adding this directory to PATH or, if you
prefer to suppress this warning, use --no-warn-script-location. The script
pydocstyle.exe is installed in 'C:\Anaconda3\envs\mne_2\Scripts' which is
not on PATH. Consider adding this directory to PATH or, if you prefer to
suppress this warning, use --no-warn-script-location. The script
codespell.exe is installed in 'C:\Anaconda3\envs\mne_2\Scripts' which is
not on PATH. Consider adding this directory to PATH or, if you prefer to
suppress this warning, use --no-warn-script-location.Successfully installed
PySurfer-0.9.0 apptools-4.4.0 bz2file-0.98 codespell-1.14.0 configobj-5.0.6
dipy-0.15.0 envisage-4.7.1 imageio-2.4.1 mayavi-4.7.0.dev0 mne-0.17.0
neo-0.7.1 nibabel-2.3.3 nilearn-0.5.0 pydocstyle-3.0.0
pytest-faulthandler-1.5.0 python-picard-0.3 quantities-0.12.2 vtk-8.1.2##
To activate this environment, use## conda activate mne\_2\#\# To deactivate an active environment, use\#\# conda deactivate*

*>>> mne.sys_info()Platform: Windows-10-10.0.17763-SP0Python:
3.7.2 (default, Jan 2 2019, 17:07:39) [MSC v.1915 64 bit
(AMD64)]Executable: C:\Anaconda3\envs\mne_2\python.exeCPU:
Intel64 Family 6 Model 158 Stepping 9, GenuineIntel: 8 coresMemory:
15.9 GBmne: 0.17.0numpy: 1.15.4 {blas=mkl_rt,
lapack=mkl_rt}scipy: 1.2.0matplotlib: 3.0.2
{backend=Qt5Agg}sklearn: 0.20.2nibabel: 2.3.3mayavi:
4.7.0.dev0 {qt_api=pyqt5, PyQt5=5.9.2}cupy: Not
foundpandas: 0.24.0dipy: 0.15.0*