[Mne_analysis] conda upgrade error
Megan Schendel
mschendel at mrn.org
Fri Sep 4 16:36:04 EDT 2020
External Email - Use Caution
Hi all,
I am getting the same PyQt5 error when I try the install via create
environment.
So attempting to creating a new environment did nothing to solve either of
the errors I was getting trying to update the environment.
In the new environment, I can import the mne module, but it doesn't have a
.__version__ attribute or a .sysinfo() attribute, so it's still broken.
I also heard back from the dipy devs that the environment line for dipy is
wrong. They suggest either drop either the first or second 'dipy', see
their response below... Has anyone had success using the environment.yml
file on the mne install page with the dipy dependency as written? I guess
I'll also try to check with the PyQt5 devs to see about the error I'm
getting on that.
Thanks for any help,
Megan
PyQt5 error...
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/mne/bin/python
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py
prepare_metadata_for_build_wheel /tmp/tmpdqxe1zsu
cwd: /tmp/pip-install-02yoibkc/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/mne/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/mne/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/mne/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/mne/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/mne/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-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/api.py",
line 51, in build_wheel
project = AbstractProject.bootstrap('pep517')
File
"/tmp/pip-build-env-6gc1wdbn/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-6gc1wdbn/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-6gc1wdbn/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-6gc1wdbn/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-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py",
line 77, in apply_user_defaults
self._get_qt_configuration()
File
"/tmp/pip-build-env-6gc1wdbn/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/mne/bin/python
/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py
prepare_metadata_for_build_wheel /tmp/tmpdqxe1zsu Check the logs for full
command output.
Using Anaconda Cloud api site https://api.anaconda.org
CondaValueError: pip returned an error.
Response from Mathew at dipy
> I don't use conda myself - but I guess that line must be wrong, and
> you need to drop either the first or the second 'dipy' , as in:
> dependencies:
> - pip:
> - --only-binary dipy
> or:
> dependencies:
> - pip:
> - dipy --only-binary
MEG Technician
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106
On Thu, Sep 3, 2020 at 5:33 PM Megan Schendel <mschendel at mrn.org> wrote:
> 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
>>>>>
>>>>> _______________________________________________
>>>>> 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
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>>>>
>>> _______________________________________________
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>
>> _______________________________________________
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>
>
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