[Mne_analysis] conda upgrade error
Megan Schendel
mschendel at mrn.org
Fri Sep 4 19:43:58 EDT 2020
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 <https://github.com/conda/conda/issues/8404>.
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
>>>>>>
>>>>> _______________________________________________
>>>>> 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
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200904/3f63db65/attachment-0001.html
More information about the Mne_analysis
mailing list