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LappalainenLab / lorals

https://lappalainenlab.github.io/lorals
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An issue with installation in conda environment #3

Closed alanlamsiu closed 2 years ago

alanlamsiu commented 3 years ago

Hi~ I was trying to set up a conda environment solely for LORALS. I first set up a conda environment, and modified the $PATH and $PYTHONPATH to inlcude the directories in the conda environment. Then I use the python setup.py install --prefix=/path/to/conda/environment to install LORALS. After that, I ran calc_ase --help. But the following error messages showed up. It would be great if you can give any suggestions on the issue.

Thansk!

Best, Xiao

"Traceback (most recent call last): File "/sc/arion/work/linx19/utilities/miniconda3/py38_4.9.2/envs/lorals/lib/python3.9/site-packages/LORALS-0.0.0-py3.9.egg/lorals/init.py", line 4, in NameError: name '__LORALS_SETUP__' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/sc/arion/work/linx19/utilities/miniconda3/py38_4.9.2/envs/lorals/bin/calc_ase", line 33, in sys.exit(load_entry_point('LORALS==0.0.0', 'console_scripts', 'calc_ase')()) File "/sc/arion/work/linx19/utilities/miniconda3/py38_4.9.2/envs/lorals/bin/calc_ase", line 25, in importlib_load_entry_point return next(matches).load() File "/sc/arion/work/linx19/utilities/miniconda3/py38_4.9.2/envs/lorals/lib/python3.9/importlib/metadata.py", line 77, in load module = import_module(match.group('module')) File "/sc/arion/work/linx19/utilities/miniconda3/py38_4.9.2/envs/lorals/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1030, in _gcd_import File "", line 1007, in _find_and_load File "", line 972, in _find_and_load_unlocked File "", line 228, in _call_with_frames_removed File "", line 1030, in _gcd_import File "", line 1007, in _find_and_load File "", line 986, in _find_and_load_unlocked File "", line 664, in _load_unlocked File "", line 627, in _load_backward_compatible File "", line 259, in load_module File "/sc/arion/work/linx19/utilities/miniconda3/py38_4.9.2/envs/lorals/lib/python3.9/site-packages/LORALS-0.0.0-py3.9.egg/lorals/init.py", line 6, in File "", line 259, in load_module File "/sc/arion/work/linx19/utilities/miniconda3/py38_4.9.2/envs/lorals/lib/python3.9/site-packages/LORALS-0.0.0-py3.9.egg/lorals/asts.py", line 15, in File "", line 259, in load_module File "/sc/arion/work/linx19/utilities/miniconda3/py38_4.9.2/envs/lorals/lib/python3.9/site-packages/LORALS-0.0.0-py3.9.egg/lorals/features.py", line 8, in File "/hpc/packages/minerva-centos7/py_packages/3.7/lib/python3.7/site-packages/pandas/init.py", line 16, in raise ImportError( ImportError: Unable to import required dependencies: numpy:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for many reasons, often due to issues with your setup or how NumPy was installed.

We have compiled some common reasons and troubleshooting tips at:

https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

and make sure that they are the versions you expect. Please carefully study the documentation linked above for further help.

Original error was: No module named 'numpy.core._multiarray_umath' "

alanlamsiu commented 2 years ago

The issue was solved by unsetting some environmental variables as below.

unset PYTHONPATH unset PERL5LIB unset R_LIBS