[Mne_analysis] conda upgrade error

Dan McCloy dan at mccloy.info
Thu Sep 3 18:15:41 EDT 2020
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        External Email - Use Caution        

If faced with this, I'd recommend creating a *new* conda environment rather than trying to update an old one. If it works cleanly, it's possible to delete the old one and rename the new one later if desired. The only reason I can think of *not* to do it this way is if your disk space is highly constrained, or if your MNE-Python environment has a lot of extra packages added that aren't in our environment.yml file (in which case it might be a bit annoying to have to manually re-install those afterward).

-- dan
Daniel McCloy
https://dan.mccloy.info
Research Scientist
Institute for Learning and Brain Sciences
University of Washington

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Thursday, September 3, 2020 5:05 PM, Megan Schendel <mschendel at mrn.org> wrote:

> External Email - Use Caution
>
> Hi Eric,
>
> Thanks for the questions. See terminal commands and outputs below. I'm on Linux.
> Since pip is listed in the environment.yml file, it should have been upgraded by the conda env -update command, right?
> In the environment I'm trying to update, mne is broken, so I can't use the python -c "import mne; mne.sys_info()" command. The results below are from the environment where I have a working mne 0.15 package, but I'm not sure which other modules have been updated there.
>
> Thanks again,
> Megan
>
> updated environment:
> pip --version
> pip 20.2.2 from /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip (python 3.8)
>
> python -c "import setuptools; print(setuptools.__version__)"
> 49.6.0.post20200814
> /updated environment
>
> old environment:
> conda --version && python --version
> conda 4.3.30
> Python 3.5.4 :: Anaconda 2.5.0 (64-bit)
> python -c "import mne; mne.sys_info()"
> Platform: Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-centos-6.7-Final
> Python: 3.5.4 |Anaconda 2.5.0 (64-bit)| (default, Aug 14 2017, 13:26:58) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
> Executable: /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/python
> CPU: x86_64: 24 cores
> Memory: 126.0 GB
>
> mne: 0.15.2
> numpy: 1.10.4 {lapack=SCIPY_MKL_H, blas=SCIPY_MKL_H}
> scipy: 0.17.0
> matplotlib: 3.0.3
>
> sklearn: 0.17.1
> nibabel: 2.3.3
> mayavi: Not found
> pycuda: Not found
> skcuda: Not found
> pandas: 0.17.1
> /old environment
>
> On Thu, Sep 3, 2020 at 3:37 PM Eric Larson <larson.eric.d at gmail.com> wrote:
>
>> External Email - Use Caution
>>
>> Building PyQt5 from source shouldn't happen. What platform are you on? Windows/Linux/macOS should in principle all work. Maybe you need to `pip install --upgrade pip`?
>>
>> Can you also try:
>>
>> $ python -c "import setuptools; print(setuptools.__version__)"
>>
>> Setuptools 50.0 has broken things in SciPy lately, it's possible there are other bugs. If it's 50.0, try `pip install "setuptools<50.0"`.
>>
>> Eric
>>
>> On Thu, Sep 3, 2020 at 5:23 PM Megan Schendel <mschendel at mrn.org> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hi all,
>>> Ok, I've asked the dipy people about that error, but I could still use help with the update.
>>> Should install instructions work for update, too? Should I just use pip to update mne instead of trying to use the new environment file?
>>>
>>> I took the dipy line out of the environment file. Here is the error I'm getting from PyQt5....
>>> Any ideas/suggestions?
>>> Thank you,
>>> Megan
>>>
>>> Collecting PyQt5>=5.10
>>> Using cached PyQt5-5.15.0.tar.gz (3.3 MB)
>>> Installing build dependencies: started
>>> Installing build dependencies: finished with status 'done'
>>> Getting requirements to build wheel: started
>>> Getting requirements to build wheel: finished with status 'done'
>>> Preparing wheel metadata: started
>>> Preparing wheel metadata: finished with status 'error'
>>> ERROR: Command errored out with exit status 1:
>>> command: /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/bin/python /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmperieq8r7
>>> cwd: /tmp/pip-install-ci617d3e/pyqt5
>>> Complete output (35 lines):
>>> Querying qmake about your Qt installation...
>>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/qmake -query
>>> Traceback (most recent call last):
>>> File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 126, in prepare_metadata_for_build_wheel
>>> hook = backend.prepare_metadata_for_build_wheel
>>> AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'
>>>
>>> During handling of the above exception, another exception occurred:
>>>
>>> Traceback (most recent call last):
>>> File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 280, in <module>
>>> main()
>>> File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 263, in main
>>> json_out['return_val'] = hook(**hook_input['kwargs'])
>>> File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 130, in prepare_metadata_for_build_wheel
>>> return _get_wheel_metadata_from_wheel(backend, metadata_directory,
>>> File "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 159, in _get_wheel_metadata_from_wheel
>>> whl_basename = backend.build_wheel(metadata_directory, config_settings)
>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/api.py", line 51, in build_wheel
>>> project = AbstractProject.bootstrap('pep517')
>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/abstract_project.py", line 82, in bootstrap
>>> project.setup(pyproject, tool, tool_description)
>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/project.py", line 479, in setup
>>> self.apply_user_defaults(tool)
>>> File "project.py", line 62, in apply_user_defaults
>>> super().apply_user_defaults(tool)
>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/project.py", line 89, in apply_user_defaults
>>> super().apply_user_defaults(tool)
>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/project.py", line 225, in apply_user_defaults
>>> self.builder.apply_user_defaults(tool)
>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py", line 77, in apply_user_defaults
>>> self._get_qt_configuration()
>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py", line 450, in _get_qt_configuration
>>> raise UserException(
>>> sipbuild.exceptions.UserException
>>> ----------------------------------------
>>> ERROR: Command errored out with exit status 1: /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/bin/python /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmperieq8r7 Check the logs for full command output.
>>> Using Anaconda Cloud api site https://api.anaconda.org
>>>
>>> CondaValueError: pip returned an error.
>>> MEG Technician
>>> The Mind Research Network
>>> 1101 Yale Blvd. NE
>>> Albuquerque, New Mexico 87106
>>>
>>> On Thu, Sep 3, 2020 at 1:18 AM Alexandre Gramfort <alexandre.gramfort at inria.fr> wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> hi Megan,
>>>>
>>>> you should ask this question to the dipy developpers. We are just users here.
>>>>
>>>> Alex
>>>>
>>>> On Thu, Sep 3, 2020 at 1:54 AM Megan Schendel <mschendel at mrn.org> wrote:
>>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> HI all,
>>>>> I'm wondering if this is an error because I already have things installed. The dipy page says to uninstall dipy before installing using pip.
>>>>> Are there separate instructions for upgrades? I realized I'm trying to follow install instructions.
>>>>>
>>>>> >>> import dipy
>>>>> >>> dipy.__file__
>>>>> '/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/dipy/__init__.py'
>>>>>
>>>>> I also tried to do the upgrade after removing the dipy line from the .yml file, but I got errors relating to PyQt
>>>>> Collecting PyQt5>=5.10
>>>>> Using cached PyQt5-5.15.0.tar.gz (3.3 MB)
>>>>> Installing build dependencies: started
>>>>> Installing build dependencies: finished with status 'done'
>>>>> Getting requirements to build wheel: started
>>>>> Getting requirements to build wheel: finished with status 'done'
>>>>> Preparing wheel metadata: started
>>>>> Preparing wheel metadata: finished with status 'error'
>>>>>
>>>>> I may have more details on the error tomorrow. I lost my connection to the remote server I'm working on.
>>>>>
>>>>> Thanks,
>>>>> Megan
>>>>> MEG Technician
>>>>> The Mind Research Network
>>>>> 1101 Yale Blvd. NE
>>>>> Albuquerque, New Mexico 87106
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Sep 2, 2020 at 4:58 PM Megan Schendel <mschendel at mrn.org> wrote:
>>>>>>
>>>>>> Hi all,
>>>>>> I am attempting to follow upgrade instructions. I was able to upgrade conda, and I succeeded in using curl to get the yml file.
>>>>>> However, when I try the conda env update, I eventually get an error when the update gets to dipy. See below. Any suggestions?
>>>>>>
>>>>>> Thanks for your help,
>>>>>> Megan
>>>>>>
>>>>>> conda env update --file environment.yml
>>>>>> Using Anaconda Cloud api site https://api.anaconda.org
>>>>>> Fetching package metadata ...........
>>>>>> Solving package specifications: .
>>>>>> ...
>>>>>> ERROR: Invalid requirement: 'dipy --only-binary dipy'
>>>>>>
>>>>>> conda --version && python --version
>>>>>> conda 4.3.30
>>>>>> Python 3.8.5
>>>>>>
>>>>>> Here is the contents of my environment.yml file:
>>>>>>
>>>>>> name: mne
>>>>>> channels:
>>>>>> - defaults
>>>>>> dependencies:
>>>>>> - python>=3.8
>>>>>> - pip
>>>>>> - numpy
>>>>>> - scipy
>>>>>> - matplotlib
>>>>>> - numba
>>>>>> - pandas
>>>>>> - xlrd
>>>>>> - scikit-learn
>>>>>> - h5py
>>>>>> - pillow
>>>>>> - statsmodels
>>>>>> - jupyter
>>>>>> - joblib
>>>>>> - psutil
>>>>>> - numexpr
>>>>>> - traits
>>>>>> - pyface
>>>>>> - traitsui
>>>>>> - imageio
>>>>>> - tqdm
>>>>>> - spyder-kernels
>>>>>> - pip:
>>>>>> - mne
>>>>>> - imageio-ffmpeg>=0.4.1
>>>>>> - vtk>=9.0.1
>>>>>> - pyvista>=0.24
>>>>>> - pyvistaqt
>>>>>> - mayavi
>>>>>> - PySurfer[save_movie]
>>>>>> - dipy --only-binary dipy
>>>>>> - nibabel
>>>>>> - nilearn
>>>>>> - neo
>>>>>> - python-picard
>>>>>> - PyQt5>=5.10,<5.14; platform_system == "Darwin"
>>>>>> - PyQt5>=5.10; platform_system != "Darwin"
>>>>>>
>>>>>> MEG Technician
>>>>>> The Mind Research Network
>>>>>> 1101 Yale Blvd. NE
>>>>>> Albuquerque, New Mexico 87106
>>>>>>
>>>>> _______________________________________________
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