scvi installing errors on get_num_classes and configure formatter 'console' #1540

2003100127 · 2022-05-13T16:35:35Z

Hi,

I am one of the scvi users. When I installed the scvi tool in a conda env, I ended up with the below errors. I tested the installation in a conda env on Windows-based and Linux-based operating systems.

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: D:\Programming\anaconda3\envs\scanal

  added / updated specs:
    - scvi-tools


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    pyjwt-2.4.0                |     pyhd8ed1ab_0          19 KB  conda-forge
    ------------------------------------------------------------
                                           Total:          19 KB

The following NEW packages will be INSTALLED:

  absl-py            conda-forge/noarch::absl-py-1.0.0-pyhd8ed1ab_0
  aiohttp            conda-forge/win-64::aiohttp-3.8.1-py38h294d835_1
  aiosignal          conda-forge/noarch::aiosignal-1.2.0-pyhd8ed1ab_0
  argon2-cffi        conda-forge/noarch::argon2-cffi-21.3.0-pyhd8ed1ab_0
  argon2-cffi-bindi~ conda-forge/win-64::argon2-cffi-bindings-21.2.0-py38h294d835_2
  asttokens          conda-forge/noarch::asttokens-2.0.5-pyhd8ed1ab_0
  async-timeout      conda-forge/noarch::async-timeout-4.0.2-pyhd8ed1ab_0
  attrs              conda-forge/noarch::attrs-21.4.0-pyhd8ed1ab_0
  backcall           conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
  backports          conda-forge/noarch::backports-1.0-py_2
  backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0
  beautifulsoup4     conda-forge/noarch::beautifulsoup4-4.11.1-pyha770c72_0
  blas               pkgs/main/win-64::blas-1.0-mkl
  bleach             conda-forge/noarch::bleach-5.0.0-pyhd8ed1ab_0
  blinker            conda-forge/noarch::blinker-1.4-py_1
  cachetools         conda-forge/noarch::cachetools-5.0.0-pyhd8ed1ab_0
  click              conda-forge/win-64::click-8.1.3-py38haa244fe_0
  commonmark         conda-forge/noarch::commonmark-0.9.1-py_0
  dataclasses        conda-forge/noarch::dataclasses-0.8-pyhc8e2a94_3
  debugpy            conda-forge/win-64::debugpy-1.6.0-py38h885f38d_0
  decorator          conda-forge/noarch::decorator-5.1.1-pyhd8ed1ab_0
  defusedxml         conda-forge/noarch::defusedxml-0.7.1-pyhd8ed1ab_0
  docrep             conda-forge/noarch::docrep-0.3.2-pyh44b312d_0
  entrypoints        conda-forge/noarch::entrypoints-0.4-pyhd8ed1ab_0
  et_xmlfile         conda-forge/noarch::et_xmlfile-1.0.1-py_1001
  executing          conda-forge/noarch::executing-0.8.3-pyhd8ed1ab_0
  flit-core          conda-forge/noarch::flit-core-3.7.1-pyhd8ed1ab_0
  frozenlist         conda-forge/win-64::frozenlist-1.3.0-py38h294d835_1
  fsspec             conda-forge/noarch::fsspec-2022.3.0-pyhd8ed1ab_0
  future             conda-forge/win-64::future-0.18.2-py38haa244fe_5
  google-auth        conda-forge/noarch::google-auth-2.6.6-pyh6c4a22f_0
  google-auth-oauth~ conda-forge/noarch::google-auth-oauthlib-0.4.6-pyhd8ed1ab_0
  grpcio             conda-forge/win-64::grpcio-1.46.1-py38he5377a8_0
  importlib_resourc~ conda-forge/noarch::importlib_resources-5.7.1-pyhd8ed1ab_0
  ipykernel          conda-forge/win-64::ipykernel-6.13.0-py38h4317176_0
  ipython            conda-forge/win-64::ipython-8.3.0-py38haa244fe_0
  ipython_genutils   conda-forge/noarch::ipython_genutils-0.2.0-py_1
  ipywidgets         conda-forge/noarch::ipywidgets-7.7.0-pyhd8ed1ab_0
  jedi               conda-forge/win-64::jedi-0.18.1-py38haa244fe_1
  jsonschema         conda-forge/noarch::jsonschema-4.5.1-pyhd8ed1ab_0
  jupyter_client     conda-forge/noarch::jupyter_client-7.3.1-pyhd8ed1ab_0
  jupyter_core       conda-forge/win-64::jupyter_core-4.10.0-py38haa244fe_0
  jupyterlab_pygmen~ conda-forge/noarch::jupyterlab_pygments-0.2.2-pyhd8ed1ab_0
  jupyterlab_widgets conda-forge/noarch::jupyterlab_widgets-1.1.0-pyhd8ed1ab_0
  libprotobuf        conda-forge/win-64::libprotobuf-3.20.1-h7755175_0
  libsodium          conda-forge/win-64::libsodium-1.0.18-h8d14728_1
  libuv              conda-forge/win-64::libuv-1.43.0-h8ffe710_0
  markdown           conda-forge/noarch::markdown-3.3.7-pyhd8ed1ab_0
  matplotlib-inline  conda-forge/noarch::matplotlib-inline-0.1.3-pyhd8ed1ab_0
  mistune            conda-forge/win-64::mistune-0.8.4-py38h294d835_1005
  mkl-service        conda-forge/win-64::mkl-service-2.4.0-py38h4f8af0f_0
  multidict          conda-forge/win-64::multidict-6.0.2-py38h294d835_1
  nbclient           conda-forge/noarch::nbclient-0.6.3-pyhd8ed1ab_0
  nbconvert          conda-forge/noarch::nbconvert-6.5.0-pyhd8ed1ab_0
  nbconvert-core     conda-forge/noarch::nbconvert-core-6.5.0-pyhd8ed1ab_0
  nbconvert-pandoc   conda-forge/noarch::nbconvert-pandoc-6.5.0-pyhd8ed1ab_0
  nbformat           conda-forge/noarch::nbformat-5.4.0-pyhd8ed1ab_0
  nest-asyncio       conda-forge/noarch::nest-asyncio-1.5.5-pyhd8ed1ab_0
  ninja              conda-forge/win-64::ninja-1.10.2-h2d74725_1
  notebook           conda-forge/noarch::notebook-6.4.11-pyha770c72_0
  oauthlib           conda-forge/noarch::oauthlib-3.2.0-pyhd8ed1ab_0
  openpyxl           conda-forge/noarch::openpyxl-3.0.9-pyhd8ed1ab_0
  opt_einsum         conda-forge/noarch::opt_einsum-3.3.0-pyhd8ed1ab_1
  pandoc             conda-forge/win-64::pandoc-2.18-h57928b3_0
  pandocfilters      conda-forge/noarch::pandocfilters-1.5.0-pyhd8ed1ab_0
  parso              conda-forge/noarch::parso-0.8.3-pyhd8ed1ab_0
  pickleshare        conda-forge/noarch::pickleshare-0.7.5-py_1003
  prometheus_client  conda-forge/noarch::prometheus_client-0.14.1-pyhd8ed1ab_0
  prompt-toolkit     conda-forge/noarch::prompt-toolkit-3.0.29-pyha770c72_0
  protobuf           conda-forge/win-64::protobuf-3.20.1-py38haa244fe_0
  psutil             conda-forge/win-64::psutil-5.9.0-py38h294d835_1
  pure_eval          conda-forge/noarch::pure_eval-0.2.2-pyhd8ed1ab_0
  pyasn1             conda-forge/noarch::pyasn1-0.4.8-py_0
  pyasn1-modules     conda-forge/noarch::pyasn1-modules-0.2.7-py_0
  pydeprecate        conda-forge/noarch::pydeprecate-0.3.0-pyhd8ed1ab_0
  pyjwt              conda-forge/noarch::pyjwt-2.4.0-pyhd8ed1ab_0
  pyro-api           conda-forge/noarch::pyro-api-0.1.2-pyhd8ed1ab_0
  pyro-ppl           conda-forge/noarch::pyro-ppl-1.8.0-pyhd8ed1ab_0
  pyrsistent         conda-forge/win-64::pyrsistent-0.18.1-py38h294d835_1
  python-fastjsonsc~ conda-forge/noarch::python-fastjsonschema-2.15.3-pyhd8ed1ab_0
  pytorch            pkgs/main/win-64::pytorch-1.10.2-cpu_py38h907fbb5_0
  pytorch-lightning  conda-forge/noarch::pytorch-lightning-1.3.8-pyhd8ed1ab_0
  pyu2f              conda-forge/noarch::pyu2f-0.1.5-pyhd8ed1ab_0
  pywin32            conda-forge/win-64::pywin32-303-py38h294d835_0
  pywinpty           conda-forge/win-64::pywinpty-0.5.7-py38haa244fe_1
  pyyaml             conda-forge/win-64::pyyaml-5.4.1-py38h294d835_1
  pyzmq              conda-forge/win-64::pyzmq-22.3.0-py38h09162b1_2
  requests-oauthlib  conda-forge/noarch::requests-oauthlib-1.3.1-pyhd8ed1ab_0
  rich               conda-forge/noarch::rich-12.4.1-pyhd8ed1ab_0
  rsa                conda-forge/noarch::rsa-4.8-pyhd8ed1ab_0
  scvi-tools         bioconda/noarch::scvi-tools-0.14.5-pyhdfd78af_0
  send2trash         conda-forge/noarch::send2trash-1.8.0-pyhd8ed1ab_0
  soupsieve          conda-forge/noarch::soupsieve-2.3.1-pyhd8ed1ab_0
  stack_data         conda-forge/noarch::stack_data-0.2.0-pyhd8ed1ab_0
  tensorboard        conda-forge/noarch::tensorboard-2.9.0-pyhd8ed1ab_0
  tensorboard-data-~ conda-forge/win-64::tensorboard-data-server-0.6.0-py38haa244fe_2
  tensorboard-plugi~ conda-forge/noarch::tensorboard-plugin-wit-1.8.1-pyhd8ed1ab_0
  terminado          conda-forge/win-64::terminado-0.9.5-py38haa244fe_0
  tinycss2           conda-forge/noarch::tinycss2-1.1.1-pyhd8ed1ab_0
  torchmetrics       conda-forge/noarch::torchmetrics-0.8.2-pyhd8ed1ab_0
  tornado            conda-forge/win-64::tornado-6.1-py38h294d835_3
  traitlets          conda-forge/noarch::traitlets-5.2.0-pyhd8ed1ab_0
  typing-extensions  conda-forge/noarch::typing-extensions-4.2.0-hd8ed1ab_1
  typing_extensions  conda-forge/noarch::typing_extensions-4.2.0-pyha770c72_1
  wcwidth            conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_2
  webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
  werkzeug           conda-forge/noarch::werkzeug-2.1.2-pyhd8ed1ab_1
  widgetsnbextension conda-forge/win-64::widgetsnbextension-3.6.0-py38haa244fe_0
  winpty             conda-forge/win-64::winpty-0.4.3-4
  yaml               conda-forge/win-64::yaml-0.2.5-h8ffe710_2
  yarl               conda-forge/win-64::yarl-1.7.2-py38h294d835_2
  zeromq             conda-forge/win-64::zeromq-4.3.4-h0e60522_1


Proceed ([y]/n)? y


Downloading and Extracting Packages
pyjwt-2.4.0          | 19 KB     | ##################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: \ Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: ok
Exception ignored in: <function Application.__del__ at 0x0000018992B59310>
Traceback (most recent call last):
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\config\application.py", line 955, in __del__
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\config\application.py", line 945, in close_handlers
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\traitlets.py", line 683, in __get__
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\traitlets.py", line 657, in get
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\traitlets.py", line 1428, in _notify_observers
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\config\application.py", line 273, in _observe_logging_default
  File "D:\Programming\anaconda3\envs\scanal\lib\site-packages\traitlets\config\application.py", line 278, in _configure_logging
  File "D:\Programming\anaconda3\envs\scanal\lib\logging\config.py", line 808, in dictConfig
  File "D:\Programming\anaconda3\envs\scanal\lib\logging\config.py", line 545, in configure
ValueError: Unable to configure formatter 'console'

done

And furthurmore I got this below when I imported scvi in the jupyter notebook.

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Input In [1], in <cell line: 1>()
----> 1 import scvi

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\scvi\__init__.py:7, in <module>
      4 import logging
      6 from ._constants import _CONSTANTS
----> 7 from ._settings import settings
      9 # this import needs to come after prior imports to prevent circular import
     10 from . import data, model, external, utils

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\scvi\_settings.py:5, in <module>
      2 from pathlib import Path
      3 from typing import Union
----> 5 import pytorch_lightning as pl
      6 import torch
      7 from rich.console import Console

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\__init__.py:20, in <module>
     17 _PACKAGE_ROOT = os.path.dirname(__file__)
     18 _PROJECT_ROOT = os.path.dirname(_PACKAGE_ROOT)
---> 20 from pytorch_lightning import metrics  # noqa: E402
     21 from pytorch_lightning.callbacks import Callback  # noqa: E402
     22 from pytorch_lightning.core import LightningDataModule, LightningModule  # noqa: E402

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\__init__.py:15, in <module>
      1 # Copyright The PyTorch Lightning team.
      2 #
      3 # Licensed under the Apache License, Version 2.0 (the "License");
   (...)
     12 # See the License for the specific language governing permissions and
     13 # limitations under the License.
---> 15 from pytorch_lightning.metrics.classification import (  # noqa: F401
     16     Accuracy,
     17     AUC,
     18     AUROC,
     19     AveragePrecision,
     20     ConfusionMatrix,
     21     F1,
     22     FBeta,
     23     HammingDistance,
     24     IoU,
     25     Precision,
     26     PrecisionRecallCurve,
     27     Recall,
     28     ROC,
     29     StatScores,
     30 )
     31 from pytorch_lightning.metrics.metric import Metric, MetricCollection  # noqa: F401
     32 from pytorch_lightning.metrics.regression import (  # noqa: F401
     33     ExplainedVariance,
     34     MeanAbsoluteError,
   (...)
     39     SSIM,
     40 )

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\classification\__init__.py:14, in <module>
      1 # Copyright The PyTorch Lightning team.
      2 #
      3 # Licensed under the Apache License, Version 2.0 (the "License");
   (...)
     12 # See the License for the specific language governing permissions and
     13 # limitations under the License.
---> 14 from pytorch_lightning.metrics.classification.accuracy import Accuracy  # noqa: F401
     15 from pytorch_lightning.metrics.classification.auc import AUC  # noqa: F401
     16 from pytorch_lightning.metrics.classification.auroc import AUROC  # noqa: F401

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\classification\accuracy.py:18, in <module>
     14 from typing import Any, Callable, Optional
     16 from torchmetrics import Accuracy as _Accuracy
---> 18 from pytorch_lightning.metrics.utils import deprecated_metrics
     21 class Accuracy(_Accuracy):
     23     @deprecated_metrics(target=_Accuracy)
     24     def __init__(
     25         self,
   (...)
     32         dist_sync_fn: Callable = None,
     33     ):

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\utils.py:22, in <module>
     20 from torchmetrics.utilities.data import dim_zero_mean as _dim_zero_mean
     21 from torchmetrics.utilities.data import dim_zero_sum as _dim_zero_sum
---> 22 from torchmetrics.utilities.data import get_num_classes as _get_num_classes
     23 from torchmetrics.utilities.data import select_topk as _select_topk
     24 from torchmetrics.utilities.data import to_categorical as _to_categorical

ImportError: cannot import name 'get_num_classes' from 'torchmetrics.utilities.data' (D:\Programming\anaconda3\envs\scanal\lib\site-packages\torchmetrics\utilities\data.py)

Please if there is any help with this issue. Thanks!

Best

The text was updated successfully, but these errors were encountered:

adamgayoso · 2022-05-13T18:26:11Z

Can you check what versions you have when you do?

In [2]: import pytorch_lightning

In [3]: pytorch_lightning.__version__
Out[3]: '1.5.8'

In [4]: import torchmetrics

In [5]: torchmetrics.__version__
Out[5]: '0.8.2'

adamgayoso · 2022-05-13T18:27:16Z

Ah actually I see what's happening, it's downloading scvi-tools 0.14.5. This is the last release we had on bioconda

https://anaconda.org/bioconda/scvi-tools

Can you ensure that conda is not searching bioconda?

You really want this (https://anaconda.org/conda-forge/scvi-tools), not the bioconda version.

AlinaKurjan · 2022-05-15T15:22:17Z

Hi, I actually have the same issue while installing scvi-tools with
conda install scvi-tools -c conda-forge
within a newly created environment with python=3.9.7

Error output after downloading and extracting packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: / Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: OK
Exception ignored in: <function Application.__del__ at 0x1044dcee0>
Traceback (most recent call last):
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/config/application.py", line 955, in __del__
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/config/application.py", line 945, in close_handlers
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/traitlets.py", line 683, in __get__
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/traitlets.py", line 657, in get
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/traitlets.py", line 1428, in _notify_observers
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/config/application.py", line 273, in _observe_logging_default
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/config/application.py", line 278, in _configure_logging
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/logging/config.py", line 809, in dictConfig
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/logging/config.py", line 546, in configure
ValueError: Unable to configure formatter 'console'

Any advice?

adamgayoso · 2022-05-15T16:22:40Z

I can look into this, I ran across it as well but even with that message, it seems to have installed successfully

2003100127 · 2022-05-15T22:14:17Z

Can you check what versions you have when you do?

In [2]: import pytorch_lightning

In [3]: pytorch_lightning.__version__
Out[3]: '1.5.8'

In [4]: import torchmetrics

In [5]: torchmetrics.__version__
Out[5]: '0.8.2'

Thanks for your quick response.
If I do

import pytorch_lightning
I got
Traceback (most recent call last):
File "", line 1, in
File "D:\Programming\anaconda3\envs\scvi-env\lib\site-packages\pytorch_lightning_init_.py", line 20, in
from pytorch_lightning import metrics # noqa: E402
File "D:\Programming\anaconda3\envs\scvi-env\lib\site-packages\pytorch_lightning\metrics_init_.py", line 15, in
from pytorch_lightning.metrics.classification import ( # noqa: F401
File "D:\Programming\anaconda3\envs\scvi-env\lib\site-packages\pytorch_lightning\metrics\classification_init_.py", line 14, in
from pytorch_lightning.metrics.classification.accuracy import Accuracy # noqa: F401
File "D:\Programming\anaconda3\envs\scvi-env\lib\site-packages\pytorch_lightning\metrics\classification\accuracy.py", line 18, in
from pytorch_lightning.metrics.utils import deprecated_metrics
File "D:\Programming\anaconda3\envs\scvi-env\lib\site-packages\pytorch_lightning\metrics\utils.py", line 22, in
from torchmetrics.utilities.data import get_num_classes as _get_num_classes
ImportError: cannot import name 'get_num_classes' from 'torchmetrics.utilities.data' (D:\Programming\anaconda3\envs\scvi-env\lib\site-packages\torchmetrics\utilities\data.py)

For torchmetrics

import torchmetrics
torchmetrics.version
'0.8.2'

2003100127 · 2022-05-15T22:17:47Z

Ah actually I see what's happening, it's downloading scvi-tools 0.14.5. This is the last release we had on bioconda

https://anaconda.org/bioconda/scvi-tools

Can you ensure that conda is not searching bioconda?

You really want this (https://anaconda.org/conda-forge/scvi-tools), not the bioconda version.

Yes, I am sure that my 2-time installations were made by using conda install -c conda-forge scvi-tools that did not work.

2003100127 · 2022-05-15T22:21:16Z

Ah actually I see what's happening, it's downloading scvi-tools 0.14.5. This is the last release we had on bioconda
https://anaconda.org/bioconda/scvi-tools
Can you ensure that conda is not searching bioconda?
You really want this (https://anaconda.org/conda-forge/scvi-tools), not the bioconda version.

Yes, I am sure that my 2-time installations were made by using conda install -c conda-forge scvi-tools that did not work.

Actually more times with python3.8 and python3.9.

adamgayoso · 2022-05-16T00:43:52Z

I see, but as you can see from the output you pasted:

  scvi-tools         bioconda/noarch::scvi-tools-0.14.5-pyhdfd78af_0

as far as I know there's a channel priority with conda, and you must have bioconda ahead of conda-forge, which is causing the issue. You can also install using pip just fine.

AlinaKurjan · 2022-05-16T11:54:53Z

as far as I know there's a channel priority with conda, and you must have bioconda ahead of conda-forge, which is causing the issue. You can also install using pip just fine.

Created a new environment again, manually changed channel priority to have conda-forge at the top before installing scvi-tools, still the same issue, unfortunately.

channel_alias: https://conda.anaconda.org
  channel_priority: flexible
  channels:
    - conda-forge
    - bioconda
    - defaults

and

  The following packages will be downloaded:
  
      package                    |            build
      ---------------------------|-----------------
      jax-0.3.12                 |     pyhd8ed1ab_0         793 KB  conda-forge
      ninja-1.11.0               |       h1b54a9f_0         128 KB  conda-forge
      ------------------------------------------------------------
                                             Total:         921 KB
  
  The following NEW packages will be INSTALLED:
  
    abseil-cpp         conda-forge/osx-64::abseil-cpp-20211102.0-h96cf925_1
    absl-py            conda-forge/noarch::absl-py-1.0.0-pyhd8ed1ab_0
    aiohttp            conda-forge/osx-64::aiohttp-3.8.1-py39h63b48b0_1
    aiosignal          conda-forge/noarch::aiosignal-1.2.0-pyhd8ed1ab_0
    anndata            conda-forge/osx-64::anndata-0.8.0-py39h6e9494a_0
    appnope            conda-forge/noarch::appnope-0.1.3-pyhd8ed1ab_0
    argon2-cffi        conda-forge/noarch::argon2-cffi-21.3.0-pyhd8ed1ab_0
    argon2-cffi-bindi~ conda-forge/osx-64::argon2-cffi-bindings-21.2.0-py39h63b48b0_2
    asttokens          conda-forge/noarch::asttokens-2.0.5-pyhd8ed1ab_0
    async-timeout      conda-forge/noarch::async-timeout-4.0.2-pyhd8ed1ab_0
    attrs              conda-forge/noarch::attrs-21.4.0-pyhd8ed1ab_0
    backcall           conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
    backports          conda-forge/noarch::backports-1.0-py_2
    backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0
    beautifulsoup4     conda-forge/noarch::beautifulsoup4-4.11.1-pyha770c72_0
    blas               pkgs/main/osx-64::blas-1.0-mkl
    bleach             conda-forge/noarch::bleach-5.0.0-pyhd8ed1ab_0
    blinker            conda-forge/noarch::blinker-1.4-py_1
    brotli             conda-forge/osx-64::brotli-1.0.9-h5eb16cf_7
    brotli-bin         conda-forge/osx-64::brotli-bin-1.0.9-h5eb16cf_7
    brotlipy           conda-forge/osx-64::brotlipy-0.7.0-py39h63b48b0_1004
    c-ares             conda-forge/osx-64::c-ares-1.18.1-h0d85af4_0
    cached-property    conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
    cached_property    conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
    cachetools         conda-forge/noarch::cachetools-5.0.0-pyhd8ed1ab_0
    certifi            conda-forge/osx-64::certifi-2021.10.8-py39h6e9494a_2
    cffi               conda-forge/osx-64::cffi-1.15.0-py39he338e87_0
    charset-normalizer conda-forge/noarch::charset-normalizer-2.0.12-pyhd8ed1ab_0
    chex               conda-forge/noarch::chex-0.1.3-pyhd8ed1ab_0
    click              conda-forge/osx-64::click-8.1.3-py39h6e9494a_0
    colorama           conda-forge/noarch::colorama-0.4.4-pyh9f0ad1d_0
    commonmark         conda-forge/noarch::commonmark-0.9.1-py_0
    cryptography       pkgs/main/osx-64::cryptography-37.0.1-py39hf6deb26_0
    cycler             conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
    dataclasses        conda-forge/noarch::dataclasses-0.8-pyhc8e2a94_3
    debugpy            conda-forge/osx-64::debugpy-1.6.0-py39hfd1d529_0
    decorator          conda-forge/noarch::decorator-5.1.1-pyhd8ed1ab_0
    defusedxml         conda-forge/noarch::defusedxml-0.7.1-pyhd8ed1ab_0
    dm-tree            conda-forge/osx-64::dm-tree-0.1.7-py39hbd61c47_0
    docrep             conda-forge/noarch::docrep-0.3.2-pyh44b312d_0
    entrypoints        conda-forge/noarch::entrypoints-0.4-pyhd8ed1ab_0
    et_xmlfile         conda-forge/noarch::et_xmlfile-1.0.1-py_1001
    executing          conda-forge/noarch::executing-0.8.3-pyhd8ed1ab_0
    flax               conda-forge/noarch::flax-0.4.1-pyhd8ed1ab_0
    flit-core          conda-forge/noarch::flit-core-3.7.1-pyhd8ed1ab_0
    fonttools          conda-forge/osx-64::fonttools-4.33.3-py39h701faf5_0
    freetype           conda-forge/osx-64::freetype-2.10.4-h4cff582_1
    frozenlist         conda-forge/osx-64::frozenlist-1.3.0-py39h63b48b0_1
    fsspec             conda-forge/noarch::fsspec-2022.3.0-pyhd8ed1ab_0
    future             conda-forge/osx-64::future-0.18.2-py39h6e9494a_5
    giflib             conda-forge/osx-64::giflib-5.2.1-hbcb3906_2
    google-auth        conda-forge/noarch::google-auth-2.6.6-pyh6c4a22f_0
    google-auth-oauth~ conda-forge/noarch::google-auth-oauthlib-0.4.6-pyhd8ed1ab_0
    grpc-cpp           conda-forge/osx-64::grpc-cpp-1.45.2-h5dcc0b3_3
    grpcio             conda-forge/osx-64::grpcio-1.46.1-py39h02843a8_0
    h5py               conda-forge/osx-64::h5py-3.2.1-nompi_py39h1bb8402_100
    hdf5               pkgs/main/osx-64::hdf5-1.10.6-hdbbcd12_0
    idna               conda-forge/noarch::idna-3.3-pyhd8ed1ab_0
    importlib-metadata conda-forge/osx-64::importlib-metadata-4.11.3-py39h6e9494a_1
    importlib_metadata conda-forge/noarch::importlib_metadata-4.11.3-hd8ed1ab_1
    importlib_resourc~ conda-forge/noarch::importlib_resources-5.7.1-pyhd8ed1ab_0
    intel-openmp       pkgs/main/osx-64::intel-openmp-2022.0.0-hecd8cb5_3615
    ipykernel          conda-forge/osx-64::ipykernel-6.13.0-py39h71a6800_0
    ipython            conda-forge/osx-64::ipython-8.3.0-py39h6e9494a_0
    ipython_genutils   conda-forge/noarch::ipython_genutils-0.2.0-py_1
    ipywidgets         conda-forge/noarch::ipywidgets-7.7.0-pyhd8ed1ab_0
    jax                conda-forge/noarch::jax-0.3.12-pyhd8ed1ab_0
    jaxlib             conda-forge/osx-64::jaxlib-0.3.7-py39h992e876_0
    jbig               conda-forge/osx-64::jbig-2.1-h0d85af4_2003
    jedi               conda-forge/osx-64::jedi-0.18.1-py39h6e9494a_1
    jinja2             conda-forge/noarch::jinja2-3.1.2-pyhd8ed1ab_0
    joblib             conda-forge/noarch::joblib-1.1.0-pyhd8ed1ab_0
    jpeg               conda-forge/osx-64::jpeg-9e-h5eb16cf_1
    jsonschema         conda-forge/noarch::jsonschema-4.5.1-pyhd8ed1ab_0
    jupyter_client     conda-forge/noarch::jupyter_client-7.3.1-pyhd8ed1ab_0
    jupyter_core       conda-forge/osx-64::jupyter_core-4.10.0-py39h6e9494a_0
    jupyterlab_pygmen~ conda-forge/noarch::jupyterlab_pygments-0.2.2-pyhd8ed1ab_0
    jupyterlab_widgets conda-forge/noarch::jupyterlab_widgets-1.1.0-pyhd8ed1ab_0
    kiwisolver         conda-forge/osx-64::kiwisolver-1.4.2-py39h7248d28_1
    lcms2              conda-forge/osx-64::lcms2-2.12-h577c468_0
    lerc               conda-forge/osx-64::lerc-3.0-he49afe7_0
    libbrotlicommon    conda-forge/osx-64::libbrotlicommon-1.0.9-h5eb16cf_7
    libbrotlidec       conda-forge/osx-64::libbrotlidec-1.0.9-h5eb16cf_7
    libbrotlienc       conda-forge/osx-64::libbrotlienc-1.0.9-h5eb16cf_7
    libcxx             conda-forge/osx-64::libcxx-14.0.3-hc203e6f_0
    libdeflate         conda-forge/osx-64::libdeflate-1.10-h0d85af4_0
    libgfortran        conda-forge/osx-64::libgfortran-3.0.1-0
    libiconv           conda-forge/osx-64::libiconv-1.16-haf1e3a3_0
    libpng             conda-forge/osx-64::libpng-1.6.37-h7cec526_2
    libprotobuf        conda-forge/osx-64::libprotobuf-3.20.1-h2292cb8_0
    libsodium          conda-forge/osx-64::libsodium-1.0.18-hbcb3906_1
    libtiff            conda-forge/osx-64::libtiff-4.3.0-h17f2ce3_3
    libwebp            conda-forge/osx-64::libwebp-1.2.2-h28dabe5_0
    libwebp-base       conda-forge/osx-64::libwebp-base-1.2.2-h0d85af4_1
    libxcb             conda-forge/osx-64::libxcb-1.13-h0d85af4_1004
    llvm-openmp        conda-forge/osx-64::llvm-openmp-14.0.3-ha654fa7_0
    lz4-c              conda-forge/osx-64::lz4-c-1.9.3-he49afe7_1
    markdown           conda-forge/noarch::markdown-3.3.7-pyhd8ed1ab_0
    markupsafe         conda-forge/osx-64::markupsafe-2.1.1-py39h63b48b0_1
    matplotlib-base    conda-forge/osx-64::matplotlib-base-3.5.2-py39h64a0072_0
    matplotlib-inline  conda-forge/noarch::matplotlib-inline-0.1.3-pyhd8ed1ab_0
    mistune            conda-forge/osx-64::mistune-0.8.4-py39h89e85a6_1005
    mkl                conda-forge/osx-64::mkl-2021.4.0-h89fa619_689
    mkl-service        conda-forge/osx-64::mkl-service-2.4.0-py39hadd8af7_0
    mkl_fft            conda-forge/osx-64::mkl_fft-1.3.1-py39h7ae3660_1
    mkl_random         conda-forge/osx-64::mkl_random-1.2.2-py39h4d6be9b_0
    msgpack-python     conda-forge/osx-64::msgpack-python-1.0.3-py39h7248d28_1
    multidict          conda-forge/osx-64::multidict-6.0.2-py39h63b48b0_1
    multipledispatch   conda-forge/noarch::multipledispatch-0.6.0-py_0
    munkres            conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
    natsort            conda-forge/noarch::natsort-8.1.0-pyhd8ed1ab_0
    nbclient           conda-forge/noarch::nbclient-0.6.3-pyhd8ed1ab_0
    nbconvert          conda-forge/noarch::nbconvert-6.5.0-pyhd8ed1ab_0
    nbconvert-core     conda-forge/noarch::nbconvert-core-6.5.0-pyhd8ed1ab_0
    nbconvert-pandoc   conda-forge/noarch::nbconvert-pandoc-6.5.0-pyhd8ed1ab_0
    nbformat           conda-forge/noarch::nbformat-5.4.0-pyhd8ed1ab_0
    nest-asyncio       conda-forge/noarch::nest-asyncio-1.5.5-pyhd8ed1ab_0
    ninja              conda-forge/osx-64::ninja-1.11.0-h1b54a9f_0
    notebook           conda-forge/noarch::notebook-6.4.11-pyha770c72_0
    numpy              pkgs/main/osx-64::numpy-1.21.5-py39h2e5f0a9_2
    numpy-base         pkgs/main/osx-64::numpy-base-1.21.5-py39h3b1a694_2
    numpyro            conda-forge/noarch::numpyro-0.9.2-pyhd8ed1ab_0
    oauthlib           conda-forge/noarch::oauthlib-3.2.0-pyhd8ed1ab_0
    openjpeg           conda-forge/osx-64::openjpeg-2.4.0-h6e7aa92_1
    openpyxl           conda-forge/noarch::openpyxl-3.0.9-pyhd8ed1ab_0
    opt_einsum         conda-forge/noarch::opt_einsum-3.3.0-pyhd8ed1ab_1
    optax              conda-forge/noarch::optax-0.1.2-pyhd8ed1ab_0
    packaging          conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
    pandas             conda-forge/osx-64::pandas-1.4.2-py39hbd61c47_1
    pandoc             conda-forge/osx-64::pandoc-2.18-h694c41f_0
    pandocfilters      conda-forge/noarch::pandocfilters-1.5.0-pyhd8ed1ab_0
    parso              conda-forge/noarch::parso-0.8.3-pyhd8ed1ab_0
    pexpect            conda-forge/noarch::pexpect-4.8.0-pyh9f0ad1d_2
    pickleshare        conda-forge/noarch::pickleshare-0.7.5-py_1003
    pillow             conda-forge/osx-64::pillow-9.1.0-py39hd2c7aa1_2
    prometheus_client  conda-forge/noarch::prometheus_client-0.14.1-pyhd8ed1ab_0
    prompt-toolkit     conda-forge/noarch::prompt-toolkit-3.0.29-pyha770c72_0
    protobuf           conda-forge/osx-64::protobuf-3.20.1-py39hd408605_0
    psutil             conda-forge/osx-64::psutil-5.9.0-py39h63b48b0_1
    pthread-stubs      conda-forge/osx-64::pthread-stubs-0.4-hc929b4f_1001
    ptyprocess         conda-forge/noarch::ptyprocess-0.7.0-pyhd3deb0d_0
    pure_eval          conda-forge/noarch::pure_eval-0.2.2-pyhd8ed1ab_0
    pyasn1             conda-forge/noarch::pyasn1-0.4.8-py_0
    pyasn1-modules     conda-forge/noarch::pyasn1-modules-0.2.7-py_0
    pycparser          conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
    pydeprecate        conda-forge/noarch::pydeprecate-0.3.2-pyhd8ed1ab_0
    pygments           conda-forge/noarch::pygments-2.12.0-pyhd8ed1ab_0
    pyjwt              conda-forge/noarch::pyjwt-2.4.0-pyhd8ed1ab_0
    pyopenssl          conda-forge/noarch::pyopenssl-22.0.0-pyhd8ed1ab_0
    pyparsing          conda-forge/noarch::pyparsing-3.0.9-pyhd8ed1ab_0
    pyro-api           conda-forge/noarch::pyro-api-0.1.2-pyhd8ed1ab_0
    pyro-ppl           conda-forge/noarch::pyro-ppl-1.8.0-pyhd8ed1ab_0
    pyrsistent         conda-forge/osx-64::pyrsistent-0.18.1-py39h63b48b0_1
    pysocks            conda-forge/osx-64::pysocks-1.7.1-py39h6e9494a_5
    python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
    python-fastjsonsc~ conda-forge/noarch::python-fastjsonschema-2.15.3-pyhd8ed1ab_0
    python-flatbuffers conda-forge/noarch::python-flatbuffers-2.0-pyhd8ed1ab_0
    pytorch            pkgs/main/osx-64::pytorch-1.10.2-cpu_py39h903acac_0
    pytorch-lightning  conda-forge/noarch::pytorch-lightning-1.5.10-pyhd8ed1ab_0
    pytz               conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
    pyu2f              conda-forge/noarch::pyu2f-0.1.5-pyhd8ed1ab_0
    pyyaml             conda-forge/osx-64::pyyaml-6.0-py39h63b48b0_4
    pyzmq              conda-forge/osx-64::pyzmq-22.3.0-py39hc2dc7ec_2
    re2                conda-forge/osx-64::re2-2022.04.01-h96cf925_0
    requests           conda-forge/noarch::requests-2.27.1-pyhd8ed1ab_0
    requests-oauthlib  conda-forge/noarch::requests-oauthlib-1.3.1-pyhd8ed1ab_0
    rich               conda-forge/noarch::rich-12.4.1-pyhd8ed1ab_0
    rsa                conda-forge/noarch::rsa-4.8-pyhd8ed1ab_0
    scikit-learn       pkgs/main/osx-64::scikit-learn-1.0.2-py39hae1ba45_1
    scipy              pkgs/main/osx-64::scipy-1.7.3-py39h8c7af03_0
    scvi-tools         conda-forge/noarch::scvi-tools-0.16.2-pyhd8ed1ab_0
    send2trash         conda-forge/noarch::send2trash-1.8.0-pyhd8ed1ab_0
    six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
    soupsieve          conda-forge/noarch::soupsieve-2.3.1-pyhd8ed1ab_0
    stack_data         conda-forge/noarch::stack_data-0.2.0-pyhd8ed1ab_0
    tbb                conda-forge/osx-64::tbb-2021.5.0-hbb4e6a2_1
    tensorboard        conda-forge/noarch::tensorboard-2.9.0-pyhd8ed1ab_0
    tensorboard-data-~ pkgs/main/osx-64::tensorboard-data-server-0.6.0-py39h5896577_0
    tensorboard-plugi~ conda-forge/noarch::tensorboard-plugin-wit-1.8.1-pyhd8ed1ab_0
    terminado          conda-forge/osx-64::terminado-0.13.3-py39h6e9494a_1
    threadpoolctl      conda-forge/noarch::threadpoolctl-3.1.0-pyh8a188c0_0
    tinycss2           conda-forge/noarch::tinycss2-1.1.1-pyhd8ed1ab_0
    toolz              conda-forge/noarch::toolz-0.11.2-pyhd8ed1ab_0
    torchmetrics       conda-forge/noarch::torchmetrics-0.8.2-pyhd8ed1ab_0
    tornado            conda-forge/osx-64::tornado-6.1-py39h63b48b0_3
    tqdm               conda-forge/noarch::tqdm-4.64.0-pyhd8ed1ab_0
    traitlets          conda-forge/noarch::traitlets-5.2.0-pyhd8ed1ab_0
    typing-extensions  conda-forge/noarch::typing-extensions-3.10.0.2-hd8ed1ab_0
    typing_extensions  conda-forge/noarch::typing_extensions-3.10.0.2-pyha770c72_0
    unicodedata2       conda-forge/osx-64::unicodedata2-14.0.0-py39h63b48b0_1
    urllib3            conda-forge/noarch::urllib3-1.26.9-pyhd8ed1ab_0
    wcwidth            conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_2
    webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
    werkzeug           conda-forge/noarch::werkzeug-2.1.2-pyhd8ed1ab_1
    widgetsnbextension conda-forge/osx-64::widgetsnbextension-3.6.0-py39h6e9494a_0
    xorg-libxau        conda-forge/osx-64::xorg-libxau-1.0.9-h35c211d_0
    xorg-libxdmcp      conda-forge/osx-64::xorg-libxdmcp-1.1.3-h35c211d_0
    yaml               conda-forge/osx-64::yaml-0.2.5-h0d85af4_2
    yarl               conda-forge/osx-64::yarl-1.7.2-py39h63b48b0_2
    zeromq             conda-forge/osx-64::zeromq-4.3.4-he49afe7_1
    zipp               conda-forge/noarch::zipp-3.8.0-pyhd8ed1ab_0
    zstd               conda-forge/osx-64::zstd-1.5.2-h582d3a0_0
  
  The following packages will be DOWNGRADED:
  
    setuptools                          62.2.0-py39h6e9494a_0 --> 59.5.0-py39h6e9494a_0`

Downloading and Extracting Packages
jax-0.3.12           | 793 KB    | ##################################################################### | 100% 
ninja-1.11.0         | 128 KB    | ##################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: \ Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: OK
Exception ignored in: <function Application.__del__ at 0x1056b7040>
Traceback (most recent call last):
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/config/application.py", line 955, in __del__
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/config/application.py", line 945, in close_handlers
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/traitlets.py", line 683, in __get__
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/traitlets.py", line 657, in get
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/traitlets.py", line 1428, in _notify_observers
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/config/application.py", line 273, in _observe_logging_default
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/traitlets/config/application.py", line 278, in _configure_logging
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/logging/config.py", line 809, in dictConfig
  File "/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/logging/config.py", line 546, in configure
ValueError: Unable to configure formatter 'console'

It does install in the end, however I get a lot of issues with packages later on, including when trying to later on install and run Spyder (Intel MKL FATAL ERROR: Cannot load libmkl_intel_thread.2.dylib.). With scvi and scanpy, I usually get the following: dlopen error with undefined symbol: H5Pset_fapl_ros3).

I do not have enough knowledge to get around those problems (fairly new to python), unfortunately, but if you have any idea about what is going on then please let me know. Thank you for your time!

AlinaKurjan · 2022-05-16T11:56:11Z

I run MacOS Moneterey 12.3.1 with Intel graphics, if it helps

AlinaKurjan · 2022-05-16T12:01:56Z

In [2]: import pytorch_lightning
In [3]: pytorch_lightning.version
Out[3]: '1.5.8'

In [4]: import torchmetrics
In [5]: torchmetrics.version
Out[5]: '0.8.2'

Mine are 1.5.10 and 0.8.2, respectively

AlinaKurjan · 2022-05-16T12:07:25Z

If I run the following in this new environment

import sys
import scvi

It shows:

ImportError: dlopen(/Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/h5py/defs.cpython-39-darwin.so, 0x0002): Symbol not found: _H5Pget_fapl_ros3
  Referenced from: /Users/akurjan/conda/obds_conda/envs/scvi-env/lib/python3.9/site-packages/h5py/defs.cpython-39-darwin.so
  Expected in: /Users/akurjan/conda/obds_conda/envs/scvi-env/lib/libhdf5.103.dylib

Packages in env:

# packages in environment at /Users/akurjan/conda/obds_conda/envs/scvi-env:
#
# Name                    Version                   Build  Channel
abseil-cpp                20211102.0           h96cf925_1    conda-forge
absl-py                   1.0.0              pyhd8ed1ab_0    conda-forge
aiohttp                   3.8.1            py39h63b48b0_1    conda-forge
aiosignal                 1.2.0              pyhd8ed1ab_0    conda-forge
anndata                   0.8.0            py39h6e9494a_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39h63b48b0_2    conda-forge
asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
blas                      1.0                         mkl  
bleach                    5.0.0              pyhd8ed1ab_0    conda-forge
blinker                   1.4                        py_1    conda-forge
brotli                    1.0.9                h5eb16cf_7    conda-forge
brotli-bin                1.0.9                h5eb16cf_7    conda-forge
brotlipy                  0.7.0           py39h63b48b0_1004    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.0.0              pyhd8ed1ab_0    conda-forge
certifi                   2021.10.8        py39h6e9494a_2    conda-forge
cffi                      1.15.0           py39he338e87_0    conda-forge
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
chex                      0.1.3              pyhd8ed1ab_0    conda-forge
click                     8.1.3            py39h6e9494a_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
commonmark                0.9.1                      py_0    conda-forge
cryptography              37.0.1           py39hf6deb26_0  
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
debugpy                   1.6.0            py39hfd1d529_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dm-tree                   0.1.7            py39hbd61c47_0    conda-forge
docrep                    0.3.2              pyh44b312d_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
et_xmlfile                1.0.1                   py_1001    conda-forge
executing                 0.8.3              pyhd8ed1ab_0    conda-forge
flax                      0.4.1              pyhd8ed1ab_0    conda-forge
flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge
fonttools                 4.33.3           py39h701faf5_0    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
frozenlist                1.3.0            py39h63b48b0_1    conda-forge
fsspec                    2022.3.0           pyhd8ed1ab_0    conda-forge
future                    0.18.2           py39h6e9494a_5    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
google-auth               2.6.6              pyh6c4a22f_0    conda-forge
google-auth-oauthlib      0.4.6              pyhd8ed1ab_0    conda-forge
grpc-cpp                  1.45.2               h5dcc0b3_3    conda-forge
grpcio                    1.46.1           py39h02843a8_0    conda-forge
h5py                      3.2.1           nompi_py39h1bb8402_100    conda-forge
hdf5                      1.10.6               hdbbcd12_0  
idna                      3.3                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.3           py39h6e9494a_1    conda-forge
importlib_metadata        4.11.3               hd8ed1ab_1    conda-forge
importlib_resources       5.7.1              pyhd8ed1ab_0    conda-forge
intel-openmp              2022.0.0          hecd8cb5_3615  
ipykernel                 6.13.0           py39h71a6800_0    conda-forge
ipython                   8.3.0            py39h6e9494a_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.7.0              pyhd8ed1ab_0    conda-forge
jax                       0.3.12             pyhd8ed1ab_0    conda-forge
jaxlib                    0.3.7            py39h992e876_0    conda-forge
jbig                      2.1               h0d85af4_2003    conda-forge
jedi                      0.18.1           py39h6e9494a_1    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_0    conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h5eb16cf_1    conda-forge
jsonschema                4.5.1              pyhd8ed1ab_0    conda-forge
jupyter_client            7.3.1              pyhd8ed1ab_0    conda-forge
jupyter_core              4.10.0           py39h6e9494a_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.1.0              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.2            py39h7248d28_1    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
lerc                      3.0                  he49afe7_0    conda-forge
libbrotlicommon           1.0.9                h5eb16cf_7    conda-forge
libbrotlidec              1.0.9                h5eb16cf_7    conda-forge
libbrotlienc              1.0.9                h5eb16cf_7    conda-forge
libcxx                    14.0.3               hc203e6f_0    conda-forge
libdeflate                1.10                 h0d85af4_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               3.0.1                         0    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
libprotobuf               3.20.1               h2292cb8_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libtiff                   4.3.0                h17f2ce3_3    conda-forge
libwebp                   1.2.2                h28dabe5_0    conda-forge
libwebp-base              1.2.2                h0d85af4_1    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libzlib                   1.2.11            h6c3fc93_1014    conda-forge
llvm-openmp               14.0.3               ha654fa7_0    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
markdown                  3.3.7              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.1            py39h63b48b0_1    conda-forge
matplotlib-base           3.5.2            py39h64a0072_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mistune                   0.8.4           py39h89e85a6_1005    conda-forge
mkl                       2021.4.0           h89fa619_689    conda-forge
mkl-service               2.4.0            py39hadd8af7_0    conda-forge
mkl_fft                   1.3.1            py39h7ae3660_1    conda-forge
mkl_random                1.2.2            py39h4d6be9b_0    conda-forge
msgpack-python            1.0.3            py39h7248d28_1    conda-forge
multidict                 6.0.2            py39h63b48b0_1    conda-forge
multipledispatch          0.6.0                      py_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
natsort                   8.1.0              pyhd8ed1ab_0    conda-forge
nbclient                  0.6.3              pyhd8ed1ab_0    conda-forge
nbconvert                 6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          6.5.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.5              pyhd8ed1ab_0    conda-forge
ninja                     1.11.0               h1b54a9f_0    conda-forge
notebook                  6.4.11             pyha770c72_0    conda-forge
numpy                     1.21.5           py39h2e5f0a9_2  
numpy-base                1.21.5           py39h3b1a694_2  
numpyro                   0.9.2              pyhd8ed1ab_0    conda-forge
oauthlib                  3.2.0              pyhd8ed1ab_0    conda-forge
openjpeg                  2.4.0                h6e7aa92_1    conda-forge
openpyxl                  3.0.9              pyhd8ed1ab_0    conda-forge
openssl                   3.0.3                hfe4f2af_0    conda-forge
opt_einsum                3.3.0              pyhd8ed1ab_1    conda-forge
optax                     0.1.2              pyhd8ed1ab_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.2            py39hbd61c47_1    conda-forge
pandoc                    2.18                 h694c41f_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.1.0            py39hd2c7aa1_2    conda-forge
pip                       22.1               pyhd8ed1ab_0    conda-forge
prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.29             pyha770c72_0    conda-forge
protobuf                  3.20.1           py39hd408605_0    conda-forge
psutil                    5.9.0            py39h63b48b0_1    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.7                      py_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydeprecate               0.3.2              pyhd8ed1ab_0    conda-forge
pygments                  2.12.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.4.0              pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyro-api                  0.1.2              pyhd8ed1ab_0    conda-forge
pyro-ppl                  1.8.0              pyhd8ed1ab_0    conda-forge
pyrsistent                0.18.1           py39h63b48b0_1    conda-forge
pysocks                   1.7.1            py39h6e9494a_5    conda-forge
python                    3.9.12          h1cc4136_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.15.3             pyhd8ed1ab_0    conda-forge
python-flatbuffers        2.0                pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytorch                   1.10.2          cpu_py39h903acac_0  
pytorch-lightning         1.5.10             pyhd8ed1ab_0    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py39h63b48b0_4    conda-forge
pyzmq                     22.3.0           py39hc2dc7ec_2    conda-forge
re2                       2022.04.01           h96cf925_0    conda-forge
readline                  8.1                  h05e3726_0    conda-forge
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    conda-forge
rich                      12.4.1             pyhd8ed1ab_0    conda-forge
rsa                       4.8                pyhd8ed1ab_0    conda-forge
scikit-learn              1.0.2            py39hae1ba45_1  
scipy                     1.7.3            py39h8c7af03_0  
scvi-tools                0.16.2             pyhd8ed1ab_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                59.5.0           py39h6e9494a_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
soupsieve                 2.3.1              pyhd8ed1ab_0    conda-forge
sqlite                    3.38.5               hd9f0692_0    conda-forge
stack_data                0.2.0              pyhd8ed1ab_0    conda-forge
tbb                       2021.5.0             hbb4e6a2_1    conda-forge
tensorboard               2.9.0              pyhd8ed1ab_0    conda-forge
tensorboard-data-server   0.6.0            py39h5896577_0  
tensorboard-plugin-wit    1.8.1              pyhd8ed1ab_0    conda-forge
terminado                 0.13.3           py39h6e9494a_1    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
toolz                     0.11.2             pyhd8ed1ab_0    conda-forge
torchmetrics              0.8.2              pyhd8ed1ab_0    conda-forge
tornado                   6.1              py39h63b48b0_3    conda-forge
tqdm                      4.64.0             pyhd8ed1ab_0    conda-forge
traitlets                 5.2.0              pyhd8ed1ab_0    conda-forge
typing-extensions         3.10.0.2             hd8ed1ab_0    conda-forge
typing_extensions         3.10.0.2           pyha770c72_0    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
unicodedata2              14.0.0           py39h63b48b0_1    conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
werkzeug                  2.1.2              pyhd8ed1ab_1    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.0            py39h6e9494a_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
yarl                      1.7.2            py39h63b48b0_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.8.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h6c3fc93_1014    conda-forge
zstd                      1.5.2                h582d3a0_0    conda-forge

adamgayoso · 2022-05-16T15:01:03Z

@AlinaKurjan can you try running conda install -c anaconda h5py in your environment?

Otherwise, I'd try a new environment, but pip install scvi-tools

AlinaKurjan · 2022-05-16T15:19:33Z

Seems to work now (with installing that anaconda h5py)! Will report if any issues spotted later on, thanks a lot for your help

2003100127 · 2022-05-18T12:03:05Z

I see, but as you can see from the output you pasted:
  scvi-tools         bioconda/noarch::scvi-tools-0.14.5-pyhdfd78af_0
as far as I know there's a channel priority with conda, and you must have bioconda ahead of conda-forge, which is causing the issue. You can also install using pip just fine.

Hi thanks for the tips on the installation. I set the highest channel_priority to conda-forge shown as following.

>conda config --set channel_priority strict
--add channels 'defaults'   # lowest priority
--add channels 'r'
--add channels 'bioconda'
--add channels 'conda-forge'   # highest priority

Then, I installed successfully scVI with its version from conda-forge scvi-tools conda-forge/noarch::scvi-tools-0.14.6-pyhd8ed1ab_0 as follows.

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: done

## Package Plan ##

  environment location: D:\Programming\anaconda3\envs\scanal

  added / updated specs:
    - scvi-tools


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    blas-1.0                   |              mkl           1 KB  conda-forge
    bzip2-1.0.8                |       h8ffe710_4         149 KB  conda-forge
    importlib_resources-5.7.1  |     pyhd8ed1ab_1          22 KB  conda-forge
    libffi-3.4.2               |       h8ffe710_5          41 KB  conda-forge
    nb_conda-2.2.1             |   py38haa244fe_4          37 KB  conda-forge
    nb_conda_kernels-2.3.1     |   py38haa244fe_1          28 KB  conda-forge
    pip-22.1                   |     pyhd8ed1ab_0         1.6 MB  conda-forge
    python-3.8.13              |h9a09f29_0_cpython        16.9 MB  conda-forge
    pywinpty-2.0.5             |   py38hd3f51b4_1         224 KB  conda-forge
    rich-12.4.1                |     pyhd8ed1ab_1         164 KB  conda-forge
    scvi-tools-0.14.6          |     pyhd8ed1ab_0         136 KB  conda-forge
    setuptools-59.5.0          |   py38haa244fe_0         1.0 MB  conda-forge
    sqlite-3.38.5              |       h8ffe710_0         1.3 MB  conda-forge
    terminado-0.15.0           |   py38haa244fe_0          28 KB  conda-forge
    testpath-0.6.0             |     pyhd8ed1ab_0          85 KB  conda-forge
    traitlets-5.2.1.post0      |     pyhd8ed1ab_0          85 KB  conda-forge
    ucrt-10.0.20348.0          |       h57928b3_0         1.2 MB  conda-forge
    vc-14.2                    |       hb210afc_6          13 KB  conda-forge
    vs2015_runtime-14.29.30037 |       h902a5da_6         1.3 MB  conda-forge
    wheel-0.37.1               |     pyhd8ed1ab_0          31 KB  conda-forge
    wincertstore-0.2           |py38haa244fe_1008          15 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        24.3 MB

The following NEW packages will be INSTALLED:

  absl-py            conda-forge/noarch::absl-py-1.0.0-pyhd8ed1ab_0
  aiohttp            conda-forge/win-64::aiohttp-3.8.1-py38h294d835_1
  aiosignal          conda-forge/noarch::aiosignal-1.2.0-pyhd8ed1ab_0
  async-timeout      conda-forge/noarch::async-timeout-4.0.2-pyhd8ed1ab_0
  backports          conda-forge/noarch::backports-1.0-py_2
  backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0
  blas               conda-forge/win-64::blas-1.0-mkl
  blinker            conda-forge/noarch::blinker-1.4-py_1
  bzip2              conda-forge/win-64::bzip2-1.0.8-h8ffe710_4
  cachetools         conda-forge/noarch::cachetools-5.0.0-pyhd8ed1ab_0
  click              conda-forge/win-64::click-8.1.3-py38haa244fe_0
  commonmark         conda-forge/noarch::commonmark-0.9.1-py_0
  dataclasses        conda-forge/noarch::dataclasses-0.8-pyhc8e2a94_3
  docrep             conda-forge/noarch::docrep-0.3.2-pyh44b312d_0
  et_xmlfile         conda-forge/noarch::et_xmlfile-1.0.1-py_1001
  flit-core          conda-forge/noarch::flit-core-3.7.1-pyhd8ed1ab_0
  frozenlist         conda-forge/win-64::frozenlist-1.3.0-py38h294d835_1
  fsspec             conda-forge/noarch::fsspec-2022.3.0-pyhd8ed1ab_0
  future             conda-forge/win-64::future-0.18.2-py38haa244fe_5
  google-auth        conda-forge/noarch::google-auth-2.6.6-pyh6c4a22f_0
  google-auth-oauth~ conda-forge/noarch::google-auth-oauthlib-0.4.6-pyhd8ed1ab_0
  grpcio             conda-forge/win-64::grpcio-1.46.1-py38he5377a8_0
  ipywidgets         conda-forge/noarch::ipywidgets-7.7.0-pyhd8ed1ab_0
  jupyterlab_widgets conda-forge/noarch::jupyterlab_widgets-1.1.0-pyhd8ed1ab_0
  libffi             conda-forge/win-64::libffi-3.4.2-h8ffe710_5
  libprotobuf        conda-forge/win-64::libprotobuf-3.20.1-h7755175_0
  libsodium          conda-forge/win-64::libsodium-1.0.18-h8d14728_1
  libuv              conda-forge/win-64::libuv-1.43.0-h8ffe710_0
  markdown           conda-forge/noarch::markdown-3.3.7-pyhd8ed1ab_0
  mkl-service        conda-forge/win-64::mkl-service-2.4.0-py38h4f8af0f_0
  multidict          conda-forge/win-64::multidict-6.0.2-py38h294d835_1
  nbconvert-core     conda-forge/noarch::nbconvert-core-6.5.0-pyhd8ed1ab_0
  nbconvert-pandoc   conda-forge/noarch::nbconvert-pandoc-6.5.0-pyhd8ed1ab_0
  ninja              conda-forge/win-64::ninja-1.11.0-h2d74725_0
  oauthlib           conda-forge/noarch::oauthlib-3.2.0-pyhd8ed1ab_0
  openpyxl           conda-forge/noarch::openpyxl-3.0.9-pyhd8ed1ab_0
  opt_einsum         conda-forge/noarch::opt_einsum-3.3.0-pyhd8ed1ab_1
  pandoc             conda-forge/win-64::pandoc-2.18-h57928b3_0
  protobuf           conda-forge/win-64::protobuf-3.20.1-py38haa244fe_0
  psutil             conda-forge/win-64::psutil-5.9.0-py38h294d835_1
  pyasn1             conda-forge/noarch::pyasn1-0.4.8-py_0
  pyasn1-modules     conda-forge/noarch::pyasn1-modules-0.2.7-py_0
  pydeprecate        conda-forge/noarch::pydeprecate-0.3.0-pyhd8ed1ab_0
  pyjwt              conda-forge/noarch::pyjwt-2.4.0-pyhd8ed1ab_0
  pyro-api           conda-forge/noarch::pyro-api-0.1.2-pyhd8ed1ab_0
  pyro-ppl           conda-forge/noarch::pyro-ppl-1.8.0-pyhd8ed1ab_0
  pytorch            pkgs/main/win-64::pytorch-1.10.2-cpu_py38h907fbb5_0
  pytorch-lightning  conda-forge/noarch::pytorch-lightning-1.3.8-pyhd8ed1ab_0
  pyu2f              conda-forge/noarch::pyu2f-0.1.5-pyhd8ed1ab_0
  pyyaml             conda-forge/win-64::pyyaml-5.4.1-py38h294d835_1
  requests-oauthlib  conda-forge/noarch::requests-oauthlib-1.3.1-pyhd8ed1ab_0
  rich               conda-forge/noarch::rich-12.4.1-pyhd8ed1ab_1
  rsa                conda-forge/noarch::rsa-4.8-pyhd8ed1ab_0
  scvi-tools         conda-forge/noarch::scvi-tools-0.14.6-pyhd8ed1ab_0
  tensorboard        conda-forge/noarch::tensorboard-2.9.0-pyhd8ed1ab_0
  tensorboard-data-~ conda-forge/win-64::tensorboard-data-server-0.6.0-py38haa244fe_2
  tensorboard-plugi~ conda-forge/noarch::tensorboard-plugin-wit-1.8.1-pyhd8ed1ab_0
  tinycss2           conda-forge/noarch::tinycss2-1.1.1-pyhd8ed1ab_0
  torchmetrics       conda-forge/noarch::torchmetrics-0.8.2-pyhd8ed1ab_0
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  werkzeug           conda-forge/noarch::werkzeug-2.1.2-pyhd8ed1ab_1
  widgetsnbextension conda-forge/win-64::widgetsnbextension-3.6.0-py38haa244fe_0
  yaml               conda-forge/win-64::yaml-0.2.5-h8ffe710_2
  yarl               conda-forge/win-64::yarl-1.7.2-py38h294d835_2
  zeromq             conda-forge/win-64::zeromq-4.3.4-h0e60522_1

The following packages will be UPDATED:

  argon2-cffi-bindi~ pkgs/main::argon2-cffi-bindings-21.2.~ --> conda-forge::argon2-cffi-bindings-21.2.0-py38h294d835_2
  bleach               pkgs/main::bleach-4.1.0-pyhd3eb1b0_0 --> conda-forge::bleach-5.0.0-pyhd8ed1ab_0
  debugpy            pkgs/main::debugpy-1.5.1-py38hd77b12b~ --> conda-forge::debugpy-1.6.0-py38h885f38d_0
  importlib_resourc~ pkgs/main::importlib_resources-5.2.0-~ --> conda-forge::importlib_resources-5.7.1-pyhd8ed1ab_1
  ipykernel          pkgs/main::ipykernel-6.9.1-py38haa955~ --> conda-forge::ipykernel-6.13.0-py38h4317176_0
  jsonschema         pkgs/main/win-64::jsonschema-4.4.0-py~ --> conda-forge/noarch::jsonschema-4.5.1-pyhd8ed1ab_0
  jupyter_client     pkgs/main/win-64::jupyter_client-7.2.~ --> conda-forge/noarch::jupyter_client-7.3.1-pyhd8ed1ab_0
  jupyterlab_pygmen~ pkgs/main::jupyterlab_pygments-0.1.2-~ --> conda-forge::jupyterlab_pygments-0.2.2-pyhd8ed1ab_0
  matplotlib-inline  pkgs/main::matplotlib-inline-0.1.2-py~ --> conda-forge::matplotlib-inline-0.1.3-pyhd8ed1ab_0
  mistune            pkgs/main::mistune-0.8.4-py38he774522~ --> conda-forge::mistune-0.8.4-py38h294d835_1005
  nb_conda                 pkgs/main::nb_conda-2.2.1-py38_1 --> conda-forge::nb_conda-2.2.1-py38haa244fe_4
  nb_conda_kernels   pkgs/main::nb_conda_kernels-2.3.1-py3~ --> conda-forge::nb_conda_kernels-2.3.1-py38haa244fe_1
  nbclient           pkgs/main/win-64::nbclient-0.5.13-py3~ --> conda-forge/noarch::nbclient-0.6.3-pyhd8ed1ab_0
  nbconvert          pkgs/main/win-64::nbconvert-6.4.4-py3~ --> conda-forge/noarch::nbconvert-6.5.0-pyhd8ed1ab_0
  nbformat           pkgs/main/win-64::nbformat-5.3.0-py38~ --> conda-forge/noarch::nbformat-5.4.0-pyhd8ed1ab_0
  pip                pkgs/main/win-64::pip-21.2.2-py38haa9~ --> conda-forge/noarch::pip-22.1-pyhd8ed1ab_0
  prometheus_client  pkgs/main::prometheus_client-0.13.1-p~ --> conda-forge::prometheus_client-0.14.1-pyhd8ed1ab_0
  prompt-toolkit     pkgs/main::prompt-toolkit-3.0.20-pyhd~ --> conda-forge::prompt-toolkit-3.0.29-pyha770c72_0
  pyrsistent         pkgs/main::pyrsistent-0.18.0-py38h196~ --> conda-forge::pyrsistent-0.18.1-py38h294d835_1
  python-fastjsonsc~ pkgs/main::python-fastjsonschema-2.15~ --> conda-forge::python-fastjsonschema-2.15.3-pyhd8ed1ab_0
  pywin32             pkgs/main::pywin32-302-py38h2bbff1b_2 --> conda-forge::pywin32-303-py38h294d835_0
  pywinpty           pkgs/main::pywinpty-2.0.2-py38h5da7b3~ --> conda-forge::pywinpty-2.0.5-py38hd3f51b4_1
  sqlite                pkgs/main::sqlite-3.38.3-h2bbff1b_0 --> conda-forge::sqlite-3.38.5-h8ffe710_0
  terminado          pkgs/main::terminado-0.13.1-py38haa95~ --> conda-forge::terminado-0.15.0-py38haa244fe_0
  testpath           pkgs/main::testpath-0.5.0-pyhd3eb1b0_0 --> conda-forge::testpath-0.6.0-pyhd8ed1ab_0
  tornado             pkgs/main::tornado-6.1-py38h2bbff1b_0 --> conda-forge::tornado-6.1-py38h294d835_3
  traitlets          pkgs/main::traitlets-5.1.1-pyhd3eb1b0~ --> conda-forge::traitlets-5.2.1.post0-pyhd8ed1ab_0
  typing-extensions  pkgs/main::typing-extensions-4.1.1-hd~ --> conda-forge::typing-extensions-4.2.0-hd8ed1ab_1
  typing_extensions  pkgs/main::typing_extensions-4.1.1-py~ --> conda-forge::typing_extensions-4.2.0-pyha770c72_1
  vc                          pkgs/main::vc-14.2-h21ff451_1 --> conda-forge::vc-14.2-hb210afc_6
  vs2015_runtime     pkgs/main::vs2015_runtime-14.27.29016~ --> conda-forge::vs2015_runtime-14.29.30037-h902a5da_6
  wcwidth             pkgs/main::wcwidth-0.2.5-pyhd3eb1b0_0 --> conda-forge::wcwidth-0.2.5-pyh9f0ad1d_2
  wincertstore       pkgs/main::wincertstore-0.2-py38haa95~ --> conda-forge::wincertstore-0.2-py38haa244fe_1008

The following packages will be SUPERSEDED by a higher-priority channel:

  argon2-cffi        pkgs/main::argon2-cffi-21.3.0-pyhd3eb~ --> conda-forge::argon2-cffi-21.3.0-pyhd8ed1ab_0
  asttokens          pkgs/main::asttokens-2.0.5-pyhd3eb1b0~ --> conda-forge::asttokens-2.0.5-pyhd8ed1ab_0
  attrs                pkgs/main::attrs-21.4.0-pyhd3eb1b0_0 --> conda-forge::attrs-21.4.0-pyhd8ed1ab_0
  backcall           pkgs/main::backcall-0.2.0-pyhd3eb1b0_0 --> conda-forge::backcall-0.2.0-pyh9f0ad1d_0
  beautifulsoup4     pkgs/main/win-64::beautifulsoup4-4.11~ --> conda-forge/noarch::beautifulsoup4-4.11.1-pyha770c72_0
  decorator          pkgs/main::decorator-5.1.1-pyhd3eb1b0~ --> conda-forge::decorator-5.1.1-pyhd8ed1ab_0
  defusedxml         pkgs/main::defusedxml-0.7.1-pyhd3eb1b~ --> conda-forge::defusedxml-0.7.1-pyhd8ed1ab_0
  entrypoints        pkgs/main/win-64::entrypoints-0.4-py3~ --> conda-forge/noarch::entrypoints-0.4-pyhd8ed1ab_0
  executing          pkgs/main::executing-0.8.3-pyhd3eb1b0~ --> conda-forge::executing-0.8.3-pyhd8ed1ab_0
  ipython            pkgs/main::ipython-8.3.0-py38haa95532~ --> conda-forge::ipython-8.3.0-py38haa244fe_0
  ipython_genutils   pkgs/main::ipython_genutils-0.2.0-pyh~ --> conda-forge::ipython_genutils-0.2.0-py_1
  jedi                pkgs/main::jedi-0.18.1-py38haa95532_1 --> conda-forge::jedi-0.18.1-py38haa244fe_1
  jupyter_core       pkgs/main::jupyter_core-4.10.0-py38ha~ --> conda-forge::jupyter_core-4.10.0-py38haa244fe_0
  nest-asyncio       pkgs/main/win-64::nest-asyncio-1.5.5-~ --> conda-forge/noarch::nest-asyncio-1.5.5-pyhd8ed1ab_0
  notebook           pkgs/main/win-64::notebook-6.4.11-py3~ --> conda-forge/noarch::notebook-6.4.11-pyha770c72_0
  pandocfilters      pkgs/main::pandocfilters-1.5.0-pyhd3e~ --> conda-forge::pandocfilters-1.5.0-pyhd8ed1ab_0
  parso                 pkgs/main::parso-0.8.3-pyhd3eb1b0_0 --> conda-forge::parso-0.8.3-pyhd8ed1ab_0
  pickleshare        pkgs/main::pickleshare-0.7.5-pyhd3eb1~ --> conda-forge::pickleshare-0.7.5-py_1003
  pure_eval          pkgs/main::pure_eval-0.2.2-pyhd3eb1b0~ --> conda-forge::pure_eval-0.2.2-pyhd8ed1ab_0
  python                pkgs/main::python-3.8.13-h6244533_0 --> conda-forge::python-3.8.13-h9a09f29_0_cpython
  pyzmq              pkgs/main::pyzmq-22.3.0-py38hd77b12b_2 --> conda-forge::pyzmq-22.3.0-py38h09162b1_2
  send2trash         pkgs/main::send2trash-1.8.0-pyhd3eb1b~ --> conda-forge::send2trash-1.8.0-pyhd8ed1ab_0
  setuptools         pkgs/main::setuptools-61.2.0-py38haa9~ --> conda-forge::setuptools-59.5.0-py38haa244fe_0
  soupsieve          pkgs/main::soupsieve-2.3.1-pyhd3eb1b0~ --> conda-forge::soupsieve-2.3.1-pyhd8ed1ab_0
  stack_data         pkgs/main::stack_data-0.2.0-pyhd3eb1b~ --> conda-forge::stack_data-0.2.0-pyhd8ed1ab_0
  webencodings       pkgs/main/win-64::webencodings-0.5.1-~ --> conda-forge/noarch::webencodings-0.5.1-py_1
  wheel                pkgs/main::wheel-0.37.1-pyhd3eb1b0_0 --> conda-forge::wheel-0.37.1-pyhd8ed1ab_0
  winpty                                          pkgs/main --> conda-forge

The following packages will be DOWNGRADED:

  libblas                                3.9.0-14_win64_mkl --> 3.9.0-12_win64_mkl
  libcblas                               3.9.0-14_win64_mkl --> 3.9.0-12_win64_mkl
  liblapack                              3.9.0-14_win64_mkl --> 3.9.0-12_win64_mkl
  mkl                                 2022.0.0-h0e2418a_796 --> 2021.4.0-h0e2418a_729


Proceed ([y]/n)? y


Downloading and Extracting Packages
wincertstore-0.2     | 15 KB     | ##################################################################################################################### | 100%
blas-1.0             | 1 KB      | ##################################################################################################################### | 100%
nb_conda-2.2.1       | 37 KB     | ##################################################################################################################### | 100%
ucrt-10.0.20348.0    | 1.2 MB    | ##################################################################################################################### | 100%
vc-14.2              | 13 KB     | ##################################################################################################################### | 100%
sqlite-3.38.5        | 1.3 MB    | ##################################################################################################################### | 100%
terminado-0.15.0     | 28 KB     | ##################################################################################################################### | 100%
scvi-tools-0.14.6    | 136 KB    | ##################################################################################################################### | 100%
nb_conda_kernels-2.3 | 28 KB     | ##################################################################################################################### | 100%
wheel-0.37.1         | 31 KB     | ##################################################################################################################### | 100%
pywinpty-2.0.5       | 224 KB    | ##################################################################################################################### | 100%
rich-12.4.1          | 164 KB    | ##################################################################################################################### | 100%
libffi-3.4.2         | 41 KB     | ##################################################################################################################### | 100%
testpath-0.6.0       | 85 KB     | ##################################################################################################################### | 100%
pip-22.1             | 1.6 MB    | ##################################################################################################################### | 100%
traitlets-5.2.1.post | 85 KB     | ##################################################################################################################### | 100%
importlib_resources- | 22 KB     | ##################################################################################################################### | 100%
setuptools-59.5.0    | 1.0 MB    | ##################################################################################################################### | 100%
python-3.8.13        | 16.9 MB   | ##################################################################################################################### | 100%
vs2015_runtime-14.29 | 1.3 MB    | ##################################################################################################################### | 100%
bzip2-1.0.8          | 149 KB    | ##################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: / Config option `kernel_spec_manager_class` not recognized by `DisableNBExtensionApp`.
Disabling notebook extension nb_conda/main...
      - Validating: ok
Disabling tree extension nb_conda/tree...
      - Validating: ok
Config option `kernel_spec_manager_class` not recognized by `DisableServerExtensionApp`.
Disabling: nb_conda
- Writing config: D:\Programming\anaconda3\envs\scanal\etc\jupyter

\ Disabling nb_conda_kernels...
CONDA_PREFIX: D:\Programming\anaconda3\envs\scanal
Status: disabled

- Enabling nb_conda_kernels...
CONDA_PREFIX: D:\Programming\anaconda3\envs\scanal
Status: enabled

\ Config option `kernel_spec_manager_class` not recognized by `EnableNBExtensionApp`.
Enabling notebook extension nb_conda/main...
      - Validating: ok
Enabling tree extension nb_conda/tree...
      - Validating: ok
Config option `kernel_spec_manager_class` not recognized by `EnableServerExtensionApp`.
Enabling: nb_conda
- Writing config: D:\Programming\anaconda3\envs\scanal\etc\jupyter
    - Validating...
      nb_conda 2.2.1 ok

- Config option `kernel_spec_manager_class` not recognized by `EnableNBExtensionApp`.
Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: ok

done

But there was still sth wrong with torchmetrics when I imported scVI, shown as follows.

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Input In [1], in <cell line: 1>()
----> 1 import scvi

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\scvi\__init__.py:7, in <module>
      4 import logging
      6 from ._constants import _CONSTANTS
----> 7 from ._settings import settings
      9 # this import needs to come after prior imports to prevent circular import
     10 from . import data, model, external, utils

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\scvi\_settings.py:5, in <module>
      2 from pathlib import Path
      3 from typing import Union
----> 5 import pytorch_lightning as pl
      6 import torch
      7 from rich.console import Console

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\__init__.py:20, in <module>
     17 _PACKAGE_ROOT = os.path.dirname(__file__)
     18 _PROJECT_ROOT = os.path.dirname(_PACKAGE_ROOT)
---> 20 from pytorch_lightning import metrics  # noqa: E402
     21 from pytorch_lightning.callbacks import Callback  # noqa: E402
     22 from pytorch_lightning.core import LightningDataModule, LightningModule  # noqa: E402

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\__init__.py:15, in <module>
      1 # Copyright The PyTorch Lightning team.
      2 #
      3 # Licensed under the Apache License, Version 2.0 (the "License");
   (...)
     12 # See the License for the specific language governing permissions and
     13 # limitations under the License.
---> 15 from pytorch_lightning.metrics.classification import (  # noqa: F401
     16     Accuracy,
     17     AUC,
     18     AUROC,
     19     AveragePrecision,
     20     ConfusionMatrix,
     21     F1,
     22     FBeta,
     23     HammingDistance,
     24     IoU,
     25     Precision,
     26     PrecisionRecallCurve,
     27     Recall,
     28     ROC,
     29     StatScores,
     30 )
     31 from pytorch_lightning.metrics.metric import Metric, MetricCollection  # noqa: F401
     32 from pytorch_lightning.metrics.regression import (  # noqa: F401
     33     ExplainedVariance,
     34     MeanAbsoluteError,
   (...)
     39     SSIM,
     40 )

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\classification\__init__.py:14, in <module>
      1 # Copyright The PyTorch Lightning team.
      2 #
      3 # Licensed under the Apache License, Version 2.0 (the "License");
   (...)
     12 # See the License for the specific language governing permissions and
     13 # limitations under the License.
---> 14 from pytorch_lightning.metrics.classification.accuracy import Accuracy  # noqa: F401
     15 from pytorch_lightning.metrics.classification.auc import AUC  # noqa: F401
     16 from pytorch_lightning.metrics.classification.auroc import AUROC  # noqa: F401

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\classification\accuracy.py:18, in <module>
     14 from typing import Any, Callable, Optional
     16 from torchmetrics import Accuracy as _Accuracy
---> 18 from pytorch_lightning.metrics.utils import deprecated_metrics
     21 class Accuracy(_Accuracy):
     23     @deprecated_metrics(target=_Accuracy)
     24     def __init__(
     25         self,
   (...)
     32         dist_sync_fn: Callable = None,
     33     ):

File D:\Programming\anaconda3\envs\scanal\lib\site-packages\pytorch_lightning\metrics\utils.py:22, in <module>
     20 from torchmetrics.utilities.data import dim_zero_mean as _dim_zero_mean
     21 from torchmetrics.utilities.data import dim_zero_sum as _dim_zero_sum
---> 22 from torchmetrics.utilities.data import get_num_classes as _get_num_classes
     23 from torchmetrics.utilities.data import select_topk as _select_topk
     24 from torchmetrics.utilities.data import to_categorical as _to_categorical

ImportError: cannot import name 'get_num_classes' from 'torchmetrics.utilities.data' (D:\Programming\anaconda3\envs\scanal\lib\site-packages\torchmetrics\utilities\data.py)

I searched online for solutions from NVIDIA/DeepLearningExamples#1113 by reinstalling a torchmetrics version=0.6.0. The installation problem is still unsolved.

adamgayoso · 2022-05-18T14:48:21Z

@2003100127 can you try with the linux-based operating system? There are some subtleties with installing on windows.

2003100127 · 2022-05-18T17:45:49Z

@2003100127 can you try with the linux-based operating system? There are some subtleties with installing on windows.

Thanks a lot for all of your useful tips. The issue is fixed. It finally succeeded on Linux or Mac but it seems problematic with Windows. The Python version made for building a successful installation of scvi-tools is 3.8.13 in my case via the conda-forge channel.

2003100127 added the bug label May 13, 2022

adamgayoso mentioned this issue May 13, 2022

ImportError due to torchmetrics theislab/cpa#2

Closed

2003100127 closed this as completed May 27, 2022

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

scvi installing errors on get_num_classes and configure formatter 'console' #1540

scvi installing errors on get_num_classes and configure formatter 'console' #1540

2003100127 commented May 13, 2022 •

edited

Loading

adamgayoso commented May 13, 2022

adamgayoso commented May 13, 2022 •

edited

Loading

AlinaKurjan commented May 15, 2022 •

edited

Loading

adamgayoso commented May 15, 2022

2003100127 commented May 15, 2022

2003100127 commented May 15, 2022

2003100127 commented May 15, 2022

adamgayoso commented May 16, 2022

AlinaKurjan commented May 16, 2022 •

edited

Loading

AlinaKurjan commented May 16, 2022

AlinaKurjan commented May 16, 2022

AlinaKurjan commented May 16, 2022 •

edited

Loading

adamgayoso commented May 16, 2022

AlinaKurjan commented May 16, 2022 •

edited

Loading

2003100127 commented May 18, 2022

adamgayoso commented May 18, 2022

2003100127 commented May 18, 2022

scvi installing errors on get_num_classes and configure formatter 'console' #1540

scvi installing errors on get_num_classes and configure formatter 'console' #1540

Comments

2003100127 commented May 13, 2022 • edited Loading

adamgayoso commented May 13, 2022

adamgayoso commented May 13, 2022 • edited Loading

AlinaKurjan commented May 15, 2022 • edited Loading

adamgayoso commented May 15, 2022

2003100127 commented May 15, 2022

2003100127 commented May 15, 2022

2003100127 commented May 15, 2022

adamgayoso commented May 16, 2022

AlinaKurjan commented May 16, 2022 • edited Loading

AlinaKurjan commented May 16, 2022

AlinaKurjan commented May 16, 2022

AlinaKurjan commented May 16, 2022 • edited Loading

adamgayoso commented May 16, 2022

AlinaKurjan commented May 16, 2022 • edited Loading

2003100127 commented May 18, 2022

adamgayoso commented May 18, 2022

2003100127 commented May 18, 2022

2003100127 commented May 13, 2022 •

edited

Loading

adamgayoso commented May 13, 2022 •

edited

Loading

AlinaKurjan commented May 15, 2022 •

edited

Loading

AlinaKurjan commented May 16, 2022 •

edited

Loading

AlinaKurjan commented May 16, 2022 •

edited

Loading

AlinaKurjan commented May 16, 2022 •

edited

Loading