[Mne_analysis] VTK Module Import Error | Anaconda Windows 10

Mar Tin beetlejuice920 at gmail.com
Fri Feb 1 06:29:15 EST 2019
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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\Rächner>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} ${PLATFORM}',
prefix: 'C:\Anaconda3\envs\mne_2', env_name: 'mne_2', mode: 'user',
used_mode: 'user'DEBUG menuinst_win32:create(320): Shortcut cmd is
C:\Anaconda3\python.exe, args are ['C:\\Anaconda3\\cwp.py',
'C:\\Anaconda3\\envs\\mne_2', 'C:\\Anaconda3\\envs\\mne_2\\python.exe',
'C:\\Anaconda3\\envs\\mne_2\\Scripts\\jupyter-notebook-script.py',
'"%USERPROFILE%/"']/ DEBUG menuinst_win32:__init__(196): Menu: name:
'Anaconda${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>
(from -r C:\Users\Rächner\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>
/ 20.8MB 6.6MB/sCollecting mne (from -r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 1))Collecting vtk
(from -r C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 2))
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>Collecting
PySurfer[save_movie] (from -r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 4))Collecting
dipy (from -r C:\Users\Rächner\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>Collecting
nibabel (from -r C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line
6))  Using cached
https://files.pythonhosted.org/packages/0a/36/a9e7ef516d0f63c2610c0033daf06c1001b1b70943f08c89d502c19bedf6/nibabel-2.3.3-py3-none-any.whl
<https://files.pythonhosted.org/packages/0a/36/a9e7ef516d0f63c2610c0033daf06c1001b1b70943f08c89d502c19bedf6/nibabel-2.3.3-py3-none-any.whl>Collecting
nilearn (from -r C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line
7))  Using cached
https://files.pythonhosted.org/packages/3d/9e/96f2da387ee9acaba2cbab7b596486b0231b5f6d9bf946b880536d4485fc/nilearn-0.5.0-py2.py3-none-any.whl
<https://files.pythonhosted.org/packages/3d/9e/96f2da387ee9acaba2cbab7b596486b0231b5f6d9bf946b880536d4485fc/nilearn-0.5.0-py2.py3-none-any.whl>Collecting
neo (from -r C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line
8))Collecting pytest-faulthandler (from -r
C:\Users\Rächner\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>Collecting
pydocstyle (from -r C:\Users\Rächner\condaenv.4puw230_.requirements.txt
(line 10))  Using cached
https://files.pythonhosted.org/packages/6e/3f/9207e1af3fb23c71a2a17a5d82d4c68f4dd6b3429b58514c74b95f6e0784/pydocstyle-3.0.0-py3-none-any.whl
<https://files.pythonhosted.org/packages/6e/3f/9207e1af3fb23c71a2a17a5d82d4c68f4dd6b3429b58514c74b95f6e0784/pydocstyle-3.0.0-py3-none-any.whl>Collecting
codespell (from -r C:\Users\Rächner\condaenv.4puw230_.requirements.txt
(line 11))Collecting python-picard (from -r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 12))Collecting
apptools (from mayavi==4.7.0.dev0->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 3))Collecting
envisage (from mayavi==4.7.0.dev0->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 3))Requirement
already satisfied: numpy in c:\anaconda3\envs\mne_2\lib\site-packages (from
mayavi==4.7.0.dev0->-r C:\Users\Rächner\condaenv.4puw230_.requirements.txt
(line 3)) (1.15.4)Requirement already satisfied: pyface>=6.0.0 in
c:\anaconda3\envs\mne_2\lib\site-packages (from mayavi==4.7.0.dev0->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 3))
(6.0.0)Requirement already satisfied: pygments in
c:\anaconda3\envs\mne_2\lib\site-packages (from mayavi==4.7.0.dev0->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 3))
(2.3.1)Requirement already satisfied: traits>=4.6.0 in
c:\anaconda3\envs\mne_2\lib\site-packages (from mayavi==4.7.0.dev0->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 3))
(4.6.0)Requirement already satisfied: traitsui>=6.0.0 in
c:\anaconda3\envs\mne_2\lib\site-packages (from mayavi==4.7.0.dev0->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 3))
(6.0.0)Requirement already satisfied: scipy in
c:\anaconda3\envs\mne_2\lib\site-packages (from PySurfer[save_movie]->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 4))
(1.2.0)Requirement already satisfied: matplotlib in
c:\anaconda3\envs\mne_2\lib\site-packages (from PySurfer[save_movie]->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 4))
(3.0.2)Collecting imageio>=1.5; extra == "save_movie" (from
PySurfer[save_movie]->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 4))Requirement
already satisfied: h5py>=2.4.0 in c:\anaconda3\envs\mne_2\lib\site-packages
(from dipy->-r C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line
5)) (2.9.0)Requirement already satisfied: six>=1.3 in
c:\anaconda3\envs\mne_2\lib\site-packages (from nibabel->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 6))
(1.12.0)Collecting bz2file (from nibabel->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 6))Collecting
quantities>=0.9.0 (from neo->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 8))Requirement
already satisfied: pytest>=2.6 in c:\anaconda3\envs\mne_2\lib\site-packages
(from pytest-faulthandler->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 9))
(4.1.1)Requirement already satisfied: snowballstemmer in
c:\anaconda3\envs\mne_2\lib\site-packages (from pydocstyle->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 10))
(1.2.1)Collecting configobj (from apptools->mayavi==4.7.0.dev0->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 3))Requirement
already satisfied: cycler>=0.10 in
c:\anaconda3\envs\mne_2\lib\site-packages (from
matplotlib->PySurfer[save_movie]->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 4))
(0.10.0)Requirement already satisfied: kiwisolver>=1.0.1 in
c:\anaconda3\envs\mne_2\lib\site-packages (from
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C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 4))
(1.0.1)Requirement already satisfied:
pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in
c:\anaconda3\envs\mne_2\lib\site-packages (from
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C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 4))
(2.3.1)Requirement already satisfied: python-dateutil>=2.1 in
c:\anaconda3\envs\mne_2\lib\site-packages (from
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C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 4))
(2.7.5)Requirement already satisfied: pillow in
c:\anaconda3\envs\mne_2\lib\site-packages (from imageio>=1.5; extra ==
"save_movie"->PySurfer[save_movie]->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 4))
(5.4.1)Requirement already satisfied: py>=1.5.0 in
c:\anaconda3\envs\mne_2\lib\site-packages (from
pytest>=2.6->pytest-faulthandler->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 9))
(1.7.0)Requirement already satisfied: setuptools in
c:\anaconda3\envs\mne_2\lib\site-packages (from
pytest>=2.6->pytest-faulthandler->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 9))
(40.6.3)Requirement already satisfied: attrs>=17.4.0 in
c:\anaconda3\envs\mne_2\lib\site-packages (from
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C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 9))
(18.2.0)Requirement already satisfied: more-itertools>=4.0.0 in
c:\anaconda3\envs\mne_2\lib\site-packages (from
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C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 9))
(5.0.0)Requirement already satisfied: atomicwrites>=1.0 in
c:\anaconda3\envs\mne_2\lib\site-packages (from
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C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 9))
(1.2.1)Requirement already satisfied: pluggy>=0.7 in
c:\anaconda3\envs\mne_2\lib\site-packages (from
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C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 9))
(0.8.1)Requirement already satisfied: colorama in
c:\anaconda3\envs\mne_2\lib\site-packages (from
pytest>=2.6->pytest-faulthandler->-r
C:\Users\Rächner\condaenv.4puw230_.requirements.txt (line 9))
(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*

Am Mo., 28. Jan. 2019, 22:31 hat Eric Larson <larson.eric.d at gmail.com>
geschrieben:

>         External Email - Use Caution
>
> 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
>
>
> On Mon, Jan 28, 2019 at 3:10 PM Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
>
>>         External Email - Use Caution
>>
>> 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
>>
>> On Sun, Jan 27, 2019 at 6:26 PM Mar Tin <beetlejuice920 at gmail.com> wrote:
>> >
>> >         External Email - Use Caution
>> >
>> > 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
>> > Am So., 27. Jan. 2019, 17:49 hat Alexandre Gramfort <
>> alexandre.gramfort at inria.fr> geschrieben:
>> >>
>> >>         External Email - Use Caution
>> >>
>> >> 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
>> >>
>> >> _______________________________________________
>> >> Mne_analysis mailing list
>> >> Mne_analysis at nmr.mgh.harvard.edu
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >
>> > _______________________________________________
>> > Mne_analysis mailing list
>> > Mne_analysis at nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
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