[Mne_analysis] conda upgrade error
Megan Schendel
mschendel at mrn.org
Thu Sep 3 19:33:08 EDT 2020
External Email - Use Caution
Hi Dan,
I tried creating a new environment, and I'm still getting the dipy error.
I'll try again removing the dipy line...
Thanks,
Megan
conda env create --name mne --file environment.yml
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata ...........
Solving package specifications: .
pyzmq-19.0.1-p 100%
|#######################################################################################################|
Time: 0:00:00 2.75 MB/s
jedi-0.17.2-py 100%
|#######################################################################################################|
Time: 0:00:00 7.84 MB/s
ERROR: Invalid requirement: 'dipy --only-binary dipy'
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 4:16 PM Dan McCloy <dan at mccloy.info> wrote:
> 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
>>>> >>
>>>> > _______________________________________________
>>>> > 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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