scanpy conda installation error

[m21camby]

I cannot install scanpy successfully. (conda v. 4.7.12)

$ conda create -n scanpy_scRNA -c bioconda scanpy
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package numba conflicts for:
scanpy -> numba[version='>=0.41.0']
Package matplotlib conflicts for:
scanpy -> matplotlib[version='3.0.*|>=2.2']
Package h5py conflicts for:
scanpy -> h5py!=2.10.0
Package networkx conflicts for:
scanpy -> networkx
Package scipy conflicts for:
scanpy -> scipy[version='<1.3|>=1.3']
Package scikit-learn conflicts for:
scanpy -> scikit-learn[version='>=0.21.2']
Package joblib conflicts for:
scanpy -> joblib
Package natsort conflicts for:
scanpy -> natsort
Package seaborn conflicts for:
scanpy -> seaborn
Package setuptools conflicts for:
scanpy -> setuptools
Package pytables conflicts for:
scanpy -> pytables
Package anndata conflicts for:
scanpy -> anndata[version='>=0.6.10|>=0.6.22rc1']
Package importlib-metadata conflicts for:
scanpy -> importlib-metadata
Package importlib_metadata conflicts for:
scanpy -> importlib_metadata[version='>=0.7']
Package tqdm conflicts for:
scanpy -> tqdm
Package pandas conflicts for:
scanpy -> pandas[version='>=0.21']
Package umap-learn conflicts for:
scanpy -> umap-learn[version='>=0.3.0']
Package patsy conflicts for:
scanpy -> patsy
Package louvain conflicts for:
scanpy -> louvain
Package python conflicts for:
scanpy -> python[version='>=3.6|>=3.6,<3.7.0a0']
Package python-igraph conflicts for:
scanpy -> python-igraph
Package statsmodels conflicts for:
scanpy -> statsmodels[version='>=0.10.0rc2']

[moldach]

I'm getting the same error from RStudio with reticulate:

From the console:

py_install('scanpy')
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - scanpy

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


Error: one or more Python packages failed to install [error code 1]

If I switch to the terminal and try pip or conda I get:

pip install scanpy

Requirement already satisfied: scanpy in /home/tsundoku/anaconda3/lib/python3.7/site-packages (1.4.5.post2)
Requirement already satisfied: setuptools-scm in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (3.3.3)
Requirement already satisfied: scipy>=1.3 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (1.3.2)
Requirement already satisfied: pandas>=0.21 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.25.3)
Requirement already satisfied: packaging in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (19.2)
Requirement already satisfied: natsort in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (7.0.0)
Requirement already satisfied: statsmodels>=0.10.0rc2 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.10.1)
Requirement already satisfied: legacy-api-wrap in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (1.2)
Requirement already satisfied: anndata>=0.6.22.post1 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.6.22.post1)
Requirement already satisfied: tqdm in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (4.40.0)
Requirement already satisfied: numba>=0.41.0 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.46.0)
Requirement already satisfied: joblib in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.14.0)
Requirement already satisfied: patsy in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.5.1)
Requirement already satisfied: importlib-metadata>=0.7; python_version < "3.8" in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy)(1.1.0)
Requirement already satisfied: tables in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (3.6.1)
Requirement already satisfied: seaborn in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.9.0)
Requirement already satisfied: networkx in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (2.4)
Requirement already satisfied: matplotlib==3.0.* in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (3.0.3)
Requirement already satisfied: h5py!=2.10.0 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (2.9.0)
Requirement already satisfied: scikit-learn>=0.21.2 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.21.3)
Requirement already satisfied: umap-learn>=0.3.10 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.3.10)
Requirement already satisfied: numpy>=1.13.3 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from pandas>=0.21->scanpy) (1.17.4)
Requirement already satisfied: pytz>=2017.2 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from pandas>=0.21->scanpy) (2019.3)
Requirement already satisfied: python-dateutil>=2.6.1 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from pandas>=0.21->scanpy) (2.8.1)
Requirement already satisfied: pyparsing>=2.0.2 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from packaging->scanpy) (2.4.5)
Requirement already satisfied: six in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from packaging->scanpy) (1.13.0)
Requirement already satisfied: setuptools in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from legacy-api-wrap->scanpy) (42.0.2.post20191203)
Requirement already satisfied: get-version>=2.0.4 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from legacy-api-wrap->scanpy) (2.1)
Requirement already satisfied: llvmlite>=0.30.0dev0 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from numba>=0.41.0->scanpy) (0.30.0)
Requirement already satisfied: zipp>=0.5 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from importlib-metadata>=0.7; python_version < "3.8"->scanpy) (0.6.0)
Requirement already satisfied: numexpr>=2.6.2 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from tables->scanpy) (2.7.0)
Requirement already satisfied: decorator>=4.3.0 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from networkx->scanpy) (4.4.1)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from matplotlib==3.0.*->scanpy) (1.1.0)
Requirement already satisfied: cycler>=0.10 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from matplotlib==3.0.*->scanpy) (0.10.0)
Requirement already satisfied: more-itertools in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from zipp>=0.5->importlib-metadata>=0.7; python_version < "3.8"->scanpy) (7.2.0)
tsundoku@tsundoku-OptiPlex-7070:~/networkanalyst/src/main/webapp/resources/data$ pip install scanpy
Requirement already satisfied: scanpy in /home/tsundoku/anaconda3/lib/python3.7/site-packages (1.4.5.post2)
Requirement already satisfied: patsy in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.5.1)
Requirement already satisfied: numba>=0.41.0 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.46.0)
Requirement already satisfied: networkx in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (2.4)
Requirement already satisfied: setuptools-scm in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (3.3.3)
Requirement already satisfied: importlib-metadata>=0.7; python_version < "3.8" in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy)(1.1.0)
Requirement already satisfied: h5py!=2.10.0 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (2.9.0)
Requirement already satisfied: seaborn in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.9.0)
Requirement already satisfied: statsmodels>=0.10.0rc2 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.10.1)
Requirement already satisfied: anndata>=0.6.22.post1 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.6.22.post1)
Requirement already satisfied: matplotlib==3.0.* in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (3.0.3)
Requirement already satisfied: pandas>=0.21 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.25.3)
Requirement already satisfied: legacy-api-wrap in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (1.2)
Requirement already satisfied: natsort in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (7.0.0)
Requirement already satisfied: tables in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (3.6.1)
Requirement already satisfied: joblib in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.14.0)
Requirement already satisfied: umap-learn>=0.3.10 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.3.10)
Requirement already satisfied: tqdm in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (4.40.0)
Requirement already satisfied: scipy>=1.3 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (1.3.2)
Requirement already satisfied: packaging in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (19.2)
Requirement already satisfied: scikit-learn>=0.21.2 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from scanpy) (0.21.3)
Requirement already satisfied: six in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from patsy->scanpy) (1.13.0)
Requirement already satisfied: numpy>=1.4 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from patsy->scanpy) (1.17.4)
Requirement already satisfied: llvmlite>=0.30.0dev0 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from numba>=0.41.0->scanpy) (0.30.0)
Requirement already satisfied: decorator>=4.3.0 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from networkx->scanpy) (4.4.1)
Requirement already satisfied: zipp>=0.5 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from importlib-metadata>=0.7; python_version < "3.8"->scanpy) (0.6.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from matplotlib==3.0.*->scanpy) (1.1.0)
Requirement already satisfied: python-dateutil>=2.1 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from matplotlib==3.0.*->scanpy) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from matplotlib==3.0.*->scanpy) (2.4.5)
Requirement already satisfied: cycler>=0.10 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from matplotlib==3.0.*->scanpy) (0.10.0)
Requirement already satisfied: pytz>=2017.2 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from pandas>=0.21->scanpy) (2019.3)
Requirement already satisfied: get-version>=2.0.4 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from legacy-api-wrap->scanpy) (2.1)
Requirement already satisfied: setuptools in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from legacy-api-wrap->scanpy) (42.0.2.post20191203)
Requirement already satisfied: numexpr>=2.6.2 in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from tables->scanpy) (2.7.0)
Requirement already satisfied: more-itertools in /home/tsundoku/anaconda3/lib/python3.7/site-packages (from zipp>=0.5->importlib-metadata>=0.7; python_version < "3.8"->scanpy) (7.2.0)

conda install -c bioconda scanpy

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: |
/
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:



Package pandas conflicts for:
scanpy -> pandas[version='>=0.21']
Package tqdm conflicts for:
scanpy -> tqdm
Package setuptools conflicts for:
scanpy -> setuptools
Package patsy conflicts for:
scanpy -> patsy
Package seaborn conflicts for:
scanpy -> seaborn
Package pytables conflicts for:
scanpy -> pytables
Package umap-learn conflicts for:
scanpy -> umap-learn[version='>=0.3.0']
Package networkx conflicts for:
scanpy -> networkx
Package readline conflicts for:
python=3.7 -> readline[version='>=7.0,<8.0a0']
Package joblib conflicts for:
scanpy -> joblib
Package importlib-metadata conflicts for:
scanpy -> importlib-metadata
Package tk conflicts for:
python=3.7 -> tk[version='>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0']
Package numba conflicts for:
scanpy -> numba[version='>=0.41.0']
Package python-igraph conflicts for:
scanpy -> python-igraph
Package libstdcxx-ng conflicts for:
python=3.7 -> libstdcxx-ng[version='>=7.2.0|>=7.3.0']
Package libffi conflicts for:
python=3.7 -> libffi[version='>=3.2.1,<4.0a0']
Package ncurses conflicts for:
python=3.7 -> ncurses[version='>=6.1,<7.0a0']
Package sqlite conflicts for:
python=3.7 -> sqlite[version='>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.29.0,<4.0a0|>=3.30.1,<4.0a0']
Package ld_impl_linux-64 conflicts for:
python=3.7 -> ld_impl_linux-64
Package statsmodels conflicts for:
scanpy -> statsmodels[version='>=0.10.0rc2']
Package zlib conflicts for:
python=3.7 -> zlib[version='>=1.2.11,<1.3.0a0']
Package louvain conflicts for:
scanpy -> louvain
Package pip conflicts for:
python=3.7 -> pip
Package h5py conflicts for:
scanpy -> h5py!=2.10.0
Package xz conflicts for:
python=3.7 -> xz[version='>=5.2.4,<6.0a0']
Package scipy conflicts for:
scanpy -> scipy[version='<1.3|>=1.3']
Package libgcc-ng conflicts for:
python=3.7 -> libgcc-ng[version='>=7.2.0|>=7.3.0']
Package anndata conflicts for:
scanpy -> anndata[version='>=0.6.10|>=0.6.22rc1']
Package matplotlib conflicts for:
scanpy -> matplotlib[version='3.0.*|>=2.2']
Package scikit-learn conflicts for:
scanpy -> scikit-learn[version='>=0.21.2']
Package natsort conflicts for:
scanpy -> natsort
Package openssl conflicts for:
python=3.7 -> openssl[version='>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a']
Package importlib_metadata conflicts for:
scanpy -> importlib_metadata[version='>=0.7']

I can import scanpy by opening Python 3 interpreter from the terminal by running python

Python 3.7.5 (default, Oct 25 2019, 15:51:11)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scanpy as sc     # this works

Check the PATH:

['', '/home/tsundoku/anaconda3/lib/python37.zip', '/home/tsundoku/anaconda3/lib/python3.7', '/home/tsundoku/anaconda3/lib/python3.7/lib-dynload', '/home/tsundoku/.local/lib/python3.7/site-packages', '/home/tsundoku/anaconda3/lib/python3.7/site-packages']

But it fails to load from reticulate

library(reticulate)
repl_python()

import pandas as pd
import scanpy as sc

ModuleNotFoundError: No module named 'scanpy'

Check the PATH:

import sys
sys.path

['', '/home/tsundoku/.local/share/r-miniconda/envs/r-reticulate/bin', '/home/tsundoku/.local/share/r-miniconda/envs/r-reticulate/lib/python36.zip', '/home/tsundoku/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6', '/home/tsundoku/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/lib-dynload', '/home/tsundoku/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages', '/home/tsundoku/R/x86_64-pc-linux-gnu-library/3.6/reticulate/python']

Okay so scanpy is installed but the PATH are different. Not sure why py_install() doesn't work. I guess the alternative is including the those paths for reticulate but not sure at the moment how to do that.

[moldach]

There is a function called reticulate::install_miniconda() which isn't mentioned in the documentation that solves this problem.

install_miniconda("scanpy")
repl_python()

import scanpy as sc  # load successfully now
exit  # close the Python interpreter 

Here's my sessionInfo() in-case it helps anyone:

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /home/tsundoku/.local/share/r-miniconda/envs/r-reticulate/lib/libmkl_rt.so

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8   
 [6] LC_MESSAGES=en_CA.UTF-8    LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] reticulate_1.14

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.2      tools_3.6.2         rappdirs_0.3.1      Rcpp_1.0.3          jsonlite_1.6        packrat_0.5.0      
[8] png_0.1-7  

[mssher07]

Having the exact same problem. Windows machine, win10, 64 bit. Trying to install from miniconda. FWIW, I have installed scanpy successfully on two other windows machines (my home computer and my work computer) in the last three weeks. Now following identical steps on my laptop and having this tissue.

conda install -c bioconda scanpy
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: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:



Package pytables conflicts for:
scanpy -> pytables
Package pandas conflicts for:
scanpy -> pandas[version='>=0.21']
Package umap-learn conflicts for:
scanpy -> umap-learn[version='>=0.3.0']
Package h5py conflicts for:
scanpy -> h5py!=2.10.0
Package patsy conflicts for:
scanpy -> patsy
Package numba conflicts for:
scanpy -> numba[version='>=0.41.0']
Package anndata conflicts for:
scanpy -> anndata[version='>=0.6.10|>=0.6.22rc1']
Package seaborn conflicts for:
scanpy -> seaborn
Package setuptools conflicts for:
scanpy -> setuptools
Package python conflicts for:
scanpy -> python[version='>=3.6']
Package importlib-metadata conflicts for:
scanpy -> importlib-metadata
Package importlib_metadata conflicts for:
scanpy -> importlib_metadata[version='>=0.7']
Package scikit-learn conflicts for:
scanpy -> scikit-learn[version='>=0.21.2']
Package networkx conflicts for:
scanpy -> networkx
Package python-igraph conflicts for:
scanpy -> python-igraph
Package louvain conflicts for:
scanpy -> louvain
Package tqdm conflicts for:
scanpy -> tqdm
Package joblib conflicts for:
scanpy -> joblib
Package natsort conflicts for:
scanpy -> natsort
Package matplotlib conflicts for:
scanpy -> matplotlib[version='3.0.*|>=2.2']
Package scipy conflicts for:
scanpy -> scipy[version='<1.3|>=1.3']
Package statsmodels conflicts for:
scanpy -> statsmodels[version='>=0.10.0rc2']

[naity]

Same issue:

UnsatisfiableError: The following specifications were found to be incompatible with each other:



Package statsmodels conflicts for:
scanpy -> statsmodels[version='>=0.10.0rc2']
Package scipy conflicts for:
scanpy -> scipy[version='<1.3|>=1.3']
Package umap-learn conflicts for:
scanpy -> umap-learn[version='>=0.3.0']
Package h5py conflicts for:
scanpy -> h5py!=2.10.0
Package importlib_metadata conflicts for:
scanpy -> importlib_metadata[version='>=0.7']
Package pip conflicts for:
python=3.6 -> pip
Package python-igraph conflicts for:
scanpy -> python-igraph
Package sqlite conflicts for:
python=3.6 -> sqlite[version='>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.26.0,<4.0a0|>=3.29.0,<4.0a0|>=3.30.1,<4.0a0']
Package openssl conflicts for:
python=3.6 -> openssl[version='1.0.*|1.0.*,>=1.0.2l,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a']
Package zlib conflicts for:
python=3.6 -> zlib[version='>=1.2.11,<1.3.0a0']
Package tk conflicts for:
python=3.6 -> tk[version='8.6.*|>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0']
Package pytables conflicts for:
scanpy -> pytables
Package tqdm conflicts for:
scanpy -> tqdm
Package patsy conflicts for:
scanpy -> patsy
Package readline conflicts for:
python=3.6 -> readline[version='7.*|>=7.0,<8.0a0']
Package setuptools conflicts for:
scanpy -> setuptools
Package anndata conflicts for:
scanpy -> anndata[version='>=0.6.10|>=0.6.22rc1']
Package libcxx conflicts for:
python=3.6 -> libcxx[version='>=4.0.1']
Package libffi conflicts for:
python=3.6 -> libffi[version='3.2.*|>=3.2.1,<4.0a0']
Package seaborn conflicts for:
scanpy -> seaborn
Package ncurses conflicts for:
python=3.6 -> ncurses[version='>=6.0,<7.0a0|>=6.1,<7.0a0']
Package scikit-learn conflicts for:
scanpy -> scikit-learn[version='>=0.21.2']
Package joblib conflicts for:
scanpy -> joblib
Package networkx conflicts for:
scanpy -> networkx
Package natsort conflicts for:
scanpy -> natsort
Package louvain conflicts for:
scanpy -> louvain
Package importlib-metadata conflicts for:
scanpy -> importlib-metadata
Package pandas conflicts for:
scanpy -> pandas[version='>=0.21']
Package numba conflicts for:
scanpy -> numba[version='>=0.41.0']
Package xz conflicts for:
python=3.6 -> xz[version='>=5.2.3,<6.0a0|>=5.2.4,<6.0a0']
Package matplotlib conflicts for:
scanpy -> matplotlib[version='3.0.*|>=2.2']

[moldach]

I was recently directed to the RStudio tutorial for setting up Python/R with {reticulate}. After this it worked successfully for me; hope it helps.

First, source the virtualenv and install the package only to the directory/project your working on (similar concept to {packrat})

Voila!

[nyoonhee]

I have the same problem. I am using macOS catalina 10.15.2

$ conda install -c bioconda scanpy

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: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package natsort conflicts for:
scanpy -> natsort
Package louvain conflicts for:
scanpy -> louvain
Package patsy conflicts for:
scanpy -> patsy
Package importlib_metadata conflicts for:
scanpy -> importlib_metadata[version='>=0.7']
Package zlib conflicts for:
python=3.7 -> zlib[version='>=1.2.11,<1.3.0a0']
Package libcxx conflicts for:
python=3.7 -> libcxx[version='>=4.0.1']
Package scikit-learn conflicts for:
scanpy -> scikit-learn[version='>=0.21.2']
Package matplotlib conflicts for:
scanpy -> matplotlib[version='3.0.*|>=2.2']
Package statsmodels conflicts for:
scanpy -> statsmodels[version='>=0.10.0rc2']
Package numba conflicts for:
scanpy -> numba[version='>=0.41.0']
Package readline conflicts for:
python=3.7 -> readline[version='>=7.0,<8.0a0']
Package importlib-metadata conflicts for:
scanpy -> importlib-metadata
Package setuptools conflicts for:
scanpy -> setuptools
Package tqdm conflicts for:
scanpy -> tqdm
Package libffi conflicts for:
python=3.7 -> libffi[version='>=3.2.1,<4.0a0']
Package scipy conflicts for:
scanpy -> scipy[version='<1.3|>=1.3']
Package anndata conflicts for:
scanpy -> anndata[version='>=0.6.10|>=0.6.22rc1']
Package pip conflicts for:
python=3.7 -> pip
Package seaborn conflicts for:
scanpy -> seaborn
Package umap-learn conflicts for:
scanpy -> umap-learn[version='>=0.3.0']
Package python-igraph conflicts for:
scanpy -> python-igraph
Package h5py conflicts for:
scanpy -> h5py!=2.10.0
Package joblib conflicts for:
scanpy -> joblib
Package networkx conflicts for:
scanpy -> networkx
Package openssl conflicts for:
python=3.7 -> openssl[version='>=1.0.2o,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a']
Package tk conflicts for:
python=3.7 -> tk[version='>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0']
Package xz conflicts for:
python=3.7 -> xz[version='>=5.2.4,<6.0a0']
Package pandas conflicts for:
scanpy -> pandas[version='>=0.21']
Package sqlite conflicts for:
python=3.7 -> sqlite[version='>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.29.0,<4.0a0|>=3.30.1,<4.0a0']
Package ncurses conflicts for:
python=3.7 -> ncurses[version='>=6.1,<7.0a0']
Package pytables conflicts for:
scanpy -> pytables

[seigfried]

Facing the same issue! Any guidance would be appreciated. Was trying to install using Anaconda Navigator for Windows but i guess I will try the Miniconda route

[cotedivoir]

Have the same issue. Windows, Ubuntu for WSL, miniconda:

conda install -c bioconda/label/cf201901 scanpy
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: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

• scanpy -> python[version='>=3.6,<3.7.0a0']

Your python: python=3.7

[kuang-da]

I had the same issue, and it turns out setting up channels solves the problem as follows:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Ref:
https://bioconda.github.io/recipes/scanpy/README.html
https://bioconda.github.io/user/install.html#set-up-channels

[cotedivoir]

Thank you! worked for me

I had the same issue, and it turns out setting up channels solves the problem as follows:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Ref:
https://bioconda.github.io/recipes/scanpy/README.html
https://bioconda.github.io/user/install.html#set-up-channels

[alirezaomidi]

Thanks, worked for me.

I had the same issue, and it turns out setting up channels solves the problem as follows:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Ref:
https://bioconda.github.io/recipes/scanpy/README.html
https://bioconda.github.io/user/install.html#set-up-channels

[kleurless]

I experienced the same issue, but none of fixes proposed here worked.
Eventually I re-installed Anaconda, immediately set up the channels, and made a new environment:

conda config --add channels default
conda config --add channels bioconda
conda config --add channels bioconda

#create a new environment
conda create --name <environment name>
#activate your environment 
conda activate <environment name>

Now that I had a new environment (which is easier to work with if you're working on multiple projects; easy switch between environments!), I tried to install scanpy again. Did not work, but then I tried it again, this time with the version number of Python, and that did the trick for me!

conda install -c bioconda scanpy python=3.7

[aedavids]

I am not sure what --add does or -c . The following is probably a cleaner way to install. It should not have any unforeseen 'channels' related side effects.

This worked for me on MacOS Catalina

$ conda create --name SCA  python=3.8.2
(base) $ conda activate SCA
(SCA) $ conda install scanpy --channel conda-forge --channel bioconda

[ryandamen]

This worked for me as well.
Amazing thanks!

I had the same issue, and it turns out setting up channels solves the problem as follows:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Ref:
https://bioconda.github.io/recipes/scanpy/README.html
https://bioconda.github.io/user/install.html#set-up-channels

[smusa]

I am not sure what --add does or -c . The following is probably a cleaner way to install. It should not have any unforeseen 'channels' related side effects.

This worked for me on MacOS Catalina

$ conda create --name SCA  python=3.8.2
(base) $ conda activate SCA
(SCA) $ conda install scanpy --channel conda-forge --channel bioconda

That's the only way it worked for me. Thanks! Without creating a virtualenv it just did not move forward.

[ckrilow]

This solution worked for me as well, thanks for the help!

[Adrilaw]

upgrade your kali linux with the command
sudo apt upgrade
pip3 install scanpy

[djwight]

I had the same issue, and it turns out setting up channels solves the problem as follows:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Ref:
https://bioconda.github.io/recipes/scanpy/README.html
https://bioconda.github.io/user/install.html#set-up-channels

Thanks, this also worked for me!