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AnantharamanLab / VIBRANT

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ERROR ./VIBRANT_setup.py -test #83

Open TaekgeunLee1 opened 11 months ago

TaekgeunLee1 commented 11 months ago

I installed Vibrant 1.2.1 via github First, I got error with Download and setup databases So I tried #39 but When I try ./VIBRANT_setup.py -test I got Error

my VIBRANT_test_setup.log

Note: NumExpr detected 20 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. NumExpr defaulting to 8 threads.

VIBRANT Caution: running a version of Scikit-Learn lower than v0.21.3 will likely cause issues. With pip you can update by running "pip install --upgrade scikit-learn==0.21.3".

But I had scikit-lean 1.3

this is my pip list Package Version

appdirs 1.4.4 biopython 1.78 boltons 23.0.0 Bottleneck 1.3.5 brotlipy 0.7.0 certifi 2023.5.7 cffi 1.15.1 charset-normalizer 2.0.4 checkv 1.0.1 conda 23.5.2 conda-content-trust 0.1.3 conda-package-handling 2.1.0 conda_package_streaming 0.8.0 contourpy 1.0.5 cryptography 39.0.1 cycler 0.11.0 Cython 3.0.0 fonttools 4.25.0 idna 3.4 importlib-metadata 6.0.0 joblib 1.3.1 jsonpatch 1.32 jsonpointer 2.1 kcounter 0.1.1 kiwisolver 1.4.4 matplotlib 3.7.1 mkl-fft 1.3.6 mkl-random 1.2.2 mkl-service 2.4.0 munkres 1.1.4 numexpr 2.8.4 numpy 1.25.0 packaging 23.0 pandas 1.5.3 pickle-mixin 1.0.2 Pillow 9.4.0 pip 23.2 pluggy 1.0.0 pooch 1.4.0 psutil 5.9.0 pycosat 0.6.4 pycparser 2.21 pyOpenSSL 23.0.0 pyparsing 3.0.9 PySocks 1.7.1 python-dateutil 2.8.2 pytz 2022.7 requests 2.29.0 ruamel.yaml 0.17.21 ruamel.yaml.clib 0.2.6 scikit-learn 1.3.0 scipy 1.10.1 seaborn 0.12.2 setuptools 67.8.0 six 1.16.0 threadpoolctl 3.2.0 toolz 0.12.0 tqdm 4.65.0 urllib3 1.26.16 wheel 0.38.4 zipp 3.11.0 zstandard 0.19.0

How can I solve this problem?

Any help is appreciated, thanks

KrisKieft commented 11 months ago

Hi, this is likely an issue with how the version of scikit-learn is verified. Please use the version listed in the README.

Acid876 commented 11 months ago

Hi, this is likely an issue with how the version of scikit-learn is verified. Please use the version listed in the README.

hi, I need to use VIBRANT in python3.8 environment, but scikit-learn 0.21.3 does not support python3.8. Is there any good way to solve this problem? Thanks~

tulikasriv26 commented 8 months ago

I am facing the same issue of scikit-learn version, have tried the higher and upgraded versionbut still same error. And scikit-learn 0.21.3 does not support python3.8

KrisKieft commented 7 months ago

What is your requirement for python v3.8?