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aertslab / create_cisTarget_databases

Create cisTarget databases
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Cannot create conda environment #18

Closed daxus4 closed 2 years ago

daxus4 commented 2 years ago

Hi everyone, I tried to create the conda environment by following the readme instruction.

When I use this command: conda create -n create_cistarget_databases \ 'python=3.8' \ 'numpy=1.19.5' \ 'pandas>=1.2.0' \ 'pyarrow>=4.0.0' \ 'numba>=0.52.0' \ 'python-flatbuffers'

I obtain this error:

Solving environment: failed

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

  • numpy=1.19.5

Current channels:

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.

Is there a workaround?

Thanks, bye!

ghuls commented 2 years ago

Yes, it should work with more recent version of numpy (numba, pyarrow, pandas and python).


conda create -n create_cistarget_databases \
 'python=3.8' \
 'numpy>=1.19.5' \ 
 'pandas>=1.2.0' \
 'pyarrow>=4.0.0' \
 'numba>=0.52.0' \
 'python-flatbuffers'
daxus4 commented 2 years ago

Thank you ghuls, now it work!

ghuls commented 2 years ago

conda create instructions are updated (It is not 100% necessary to have those versions, as older versions should also work).

TingTingShao commented 2 months ago

Hi,

with 

conda create -n create_cistarget_databases \
    'python=3.10' \
    'numpy=1.21' \
    'pandas>=1.4.1' \
    'pyarrow>=7.0.0' \
    'numba>=0.55.1' \
    'python-flatbuffers'

The error occurs:

(create_cistarget_databases) bash-4.4$ $VSC_DATA/create_cisTarget_databases/create_cistarget_motif_databases.py -h
Traceback (most recent call last):
  File "/data/leuven/351/vsc35107/miniconda3/envs/create_cistarget_databases/lib/python3.10/site-packages/pandas/__init__.py", line 23, in <module>
    from pandas.compat import (
  File "/data/leuven/351/vsc35107/miniconda3/envs/create_cistarget_databases/lib/python3.10/site-packages/pandas/compat/__init__.py", line 26, in <module>
    from pandas.compat.numpy import is_numpy_dev
  File "/data/leuven/351/vsc35107/miniconda3/envs/create_cistarget_databases/lib/python3.10/site-packages/pandas/compat/numpy/__init__.py", line 20, in <module>
    raise ImportError(
ImportError: this version of pandas is incompatible with numpy < 1.22.4
your numpy version is 1.21.6.
Please upgrade numpy to >= 1.22.4 to use this pandas version

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/data/leuven/351/vsc35107/create_cisTarget_databases/create_cistarget_motif_databases.py", line 19, in <module>
    import pandas as pd
  File "/data/leuven/351/vsc35107/miniconda3/envs/create_cistarget_databases/lib/python3.10/site-packages/pandas/__init__.py", line 28, in <module>
    raise ImportError(
ImportError: C extension: None not built. If you want to import pandas from the source directory, you may need to run 'python setup.py build_ext' to build the C extensions first.

Should I try the other version:

conda create -n create_cistarget_databases \
 'python=3.8' \
 'numpy>=1.19.5' \ 
 'pandas>=1.2.0' \
 'pyarrow>=4.0.0' \
 'numba>=0.52.0' \
 'python-flatbuffers'

Thanks, tingting