[Mne_analysis] conda upgrade error
Megan Schendel
mschendel at mrn.org
Tue Sep 8 18:01:55 EDT 2020
External Email - Use Caution
Hi Alexandre, Eric,
Thanks for the responses.
I will see what I can accomplish without the offending packages (I got dipy
to install, but no luck with PyQt yet). I was trying to help a
colleague with the Visualize Source Time Courses tutorial, so we'll see
what errors we run into.
I found an anaconda user group, so I will ask them about why I cannot seem
to update my conda version.
Thanks again,
Megan
MEG Technician
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106
On Sat, Sep 5, 2020 at 11:00 AM Eric Larson <larson.eric.d at gmail.com> wrote:
> External Email - Use Caution
>
> I would just remove the `dipy` line from the environment file to see if
> that will install properly. If it doesn't, you could iteratively remove
> requirements or as Alex says, try just installing numpy, scipy, matplotlib,
> and mne.
>
> FYI CentOS 6 reaches end-of-life for even security updates in November, so
> it might not be a bad time to consider upgrading. (Of course this is not
> the easiest solution, though!)
>
> Eric
>
>
>
> On Sat, Sep 5, 2020 at 7:52 AM Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
>
>> External Email - Use Caution
>>
>> hi Megan,
>>
>> thanks for the details. Unfortunately it's going to be really hard to
>> debug for us
>> without accessing your system. Note however that you can still use
>> mne-python
>> with just numpy, scipy and matplotlib. It will cover 90% of what you can
>> do with
>> mne-python. What you will not have is 3D support but if it's remove
>> compute
>> cluster maybe it's not a real issue.
>>
>> Alex
>>
>>
>>
>>
>> On Sat, Sep 5, 2020 at 1:45 AM Megan Schendel <mschendel at mrn.org> wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi all,
>> > The PyQt5 list helped me track down that error a bit more. The wheel
>> build for PyQt5 depends on something called manylinux2014, which depends on
>> CentOS7. The server I'm trying to use is CentOS 6.7.
>> >
>> > It sounds like my environment/pip dipy issue is related to the anaconda
>> version I have (may also be why mne was broken when I tried to create the
>> environment).
>> > There are issues with the environment file using pip in older anaconda
>> versions.
>> > However, this is after I do "conda update --all" in my mne
>> environment. I'm having trouble figuring out how to get a newer anaconda
>> package. The mne install page suggests conda version 4.6.2. It looks like
>> I have 4.3.30. The github issue page says the pip options issue is fixed
>> with 4.6.9
>> > Sorry to ask a conda question here, but when I try "conda update
>> anaconda" I get an error saying "PackageNotInstalledError: Package is not
>> installed in prefix." From searching, it sounds like I need to update my
>> base/root anaconda environment, but I'm not sure I want to do that?
>> >
>> > Also, FWIW I was able to get dipy to install using "pip install dipy
>> --only-binary dipy", which sort of led me down the rabbit hole of why my
>> environment didn't seem to be working with the pip options... I was also
>> able to install mne using pip.
>> >
>> > Just thought I'd update. It seems it is an issue with my system, not
>> with your environment file.
>> > Thanks,
>> > Megan
>> >
>> > conda info
>> > Current conda install:
>> >
>> > platform : linux-64
>> > conda version : 4.3.30
>> > conda is private : False
>> > conda-env version : 4.3.30
>> > conda-build version : 1.19.0
>> > python version : 3.5.4.final.0
>> > requests version : 2.12.4
>> > root environment :
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3
>> (writable)
>> > default environment :
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne
>> > envs directories :
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs
>> > /na/homes/mschendel/.conda/envs
>> > package cache :
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/pkgs
>> > /na/homes/mschendel/.conda/pkgs
>> > channel URLs : https://repo.continuum.io/pkgs/main/linux-64
>> > https://repo.continuum.io/pkgs/main/noarch
>> > https://repo.continuum.io/pkgs/free/linux-64
>> > https://repo.continuum.io/pkgs/free/noarch
>> > https://repo.continuum.io/pkgs/r/linux-64
>> > https://repo.continuum.io/pkgs/r/noarch
>> > https://repo.continuum.io/pkgs/pro/linux-64
>> > https://repo.continuum.io/pkgs/pro/noarch
>> > config file : None
>> > netrc file : None
>> > offline mode : False
>> > user-agent : conda/4.3.30 requests/2.12.4 CPython/3.5.4
>> Linux/2.6.32-573.7.1.el6.x86_64 CentOS/6.7 glibc/2.12
>> > UID:GID : 10263:8000
>> >
>> >
>> > I was able to get dipy to install...
>> >
>> > (mne) [mschendel at earth python]$ pip --version
>> > pip 20.2.2 from
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip
>> (python 3.8)
>> >
>> > (mne) [mschendel at earth envs]$ pip install dipy --only-binary dipy
>> > Collecting dipy
>> > Using cached dipy-1.1.1-cp38-cp38-manylinux1_x86_64.whl (8.0 MB)
>> > Collecting nibabel>=3.0.0
>> > Using cached nibabel-3.1.1-py3-none-any.whl (3.3 MB)
>> > Requirement already satisfied: scipy>=1.0 in
>> ./mne/lib/python3.8/site-packages (from dipy) (1.5.2)
>> > Requirement already satisfied: h5py>=2.4.0 in
>> ./mne/lib/python3.8/site-packages (from dipy) (2.10.0)
>> > Requirement already satisfied: numpy>=1.13 in
>> ./mne/lib/python3.8/site-packages (from nibabel>=3.0.0->dipy) (1.19.1)
>> > Requirement already satisfied: packaging>=14.3 in
>> ./mne/lib/python3.8/site-packages (from nibabel>=3.0.0->dipy) (20.4)
>> > Requirement already satisfied: six in ./mne/lib/python3.8/site-packages
>> (from h5py>=2.4.0->dipy) (1.15.0)
>> > Requirement already satisfied: pyparsing>=2.0.2 in
>> ./mne/lib/python3.8/site-packages (from
>> packaging>=14.3->nibabel>=3.0.0->dipy) (2.4.7)
>> > Installing collected packages: nibabel, dipy
>> > Successfully installed dipy-1.1.1 nibabel-3.1.1
>> >
>> > Here's where I am now:
>> > mne.sys_info()
>> > Platform: Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-glibc2.10
>> > Python: 3.8.5 (default, Sep 4 2020, 07:30:14) [GCC 7.3.0]
>> > Executable:
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/bin/python3
>> > CPU: x86_64: 24 cores
>> > Memory: 126.0 GB
>> >
>> > mne: 0.20.8
>> > numpy: 1.19.1 {blas=mkl_rt, lapack=mkl_rt}
>> > scipy: 1.5.2
>> > matplotlib: 3.3.1 {backend=agg}
>> >
>> > sklearn: 0.23.2
>> > numba: 0.50.1
>> > nibabel: 3.1.1
>> > cupy: Not found
>> > pandas: 1.1.1
>> > dipy: 1.1.1
>> > mayavi: Not found
>> > pyvista: Not found
>> > vtk: Not found
>> >
>> >
>> > MEG Technician
>> > The Mind Research Network
>> > 1101 Yale Blvd. NE
>> > Albuquerque, New Mexico 87106
>> >
>> >
>> >
>> > On Fri, Sep 4, 2020 at 2:36 PM Megan Schendel <mschendel at mrn.org>
>> wrote:
>> >>
>> >> 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
>> >>>>>>
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