[Mne_analysis] conda upgrade error
Eric Larson
larson.eric.d at gmail.com
Thu Sep 3 17:35:36 EDT 2020
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
>> >>
>> > _______________________________________________
>> > Mne_analysis mailing list
>> > Mne_analysis at nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
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