EntityLinker import not working

Hi everyone,

I’m unable to import the scispacy EntityLinker using the code:

import spacy
import scispacy

from scispacy.linking import EntityLinker

When I run this piece of code in the Jupyter lab, the cell does not run and probably the kernel dies or restarts. I’m not sure what exactly is happening.

Details which might be useful:

Please also find the packages installed in the environment:

# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: osx-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/osx-64/_py-xgboost-mutex-2.0-cpu_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/blas-1.0-mkl.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/c-ares-1.17.1-h0d85af4_1.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/ca-certificates-2021.5.25-hecd8cb5_1.conda
https://conda.anaconda.org/anaconda/osx-64/fribidi-1.0.10-haf1e3a3_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/intel-openmp-2021.2.0-hecd8cb5_564.conda
https://conda.anaconda.org/anaconda/osx-64/jpeg-9b-he5867d9_2.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/libcxx-11.1.0-habf9029_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/libgfortran-3.0.1-h93005f0_2.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/libiconv-1.16-h1de35cc_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/libsodium-1.0.18-h1de35cc_0.conda
https://conda.anaconda.org/conda-forge/osx-64/llvm-openmp-11.1.0-hda6cdc1_1.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/pandoc-2.12-hecd8cb5_0.conda
https://conda.anaconda.org/anaconda/osx-64/pixman-0.40.0-haf1e3a3_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/xz-5.2.5-h1de35cc_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/yaml-0.2.5-haf1e3a3_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/zlib-1.2.11-h1de35cc_3.conda
https://repo.anaconda.com/pkgs/main/osx-64/expat-2.3.0-h23ab428_2.conda
https://conda.anaconda.org/anaconda/osx-64/graphite2-1.3.14-h38d11af_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/hdf5-1.10.6-hdbbcd12_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/icu-58.2-h0a44026_3.conda
https://conda.anaconda.org/conda-forge/osx-64/libcrc32c-1.1.1-h1c7c35f_2.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/libffi-3.3-hb1e8313_2.conda
https://repo.anaconda.com/pkgs/main/osx-64/libllvm10-10.0.1-h76017ad_5.conda
https://conda.anaconda.org/anaconda/osx-64/libpng-1.6.37-ha441bb4_0.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/libprotobuf-3.16.0-hcf210ce_0.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/libxgboost-1.4.0-he49afe7_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/lz4-c-1.9.2-h79c402e_3.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/mkl-2021.2.0-hecd8cb5_269.conda
https://repo.anaconda.com/pkgs/main/osx-64/ncurses-6.2-h0a44026_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/nodejs-10.13.0-h0a44026_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/openssl-1.1.1k-h9ed2024_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/pcre-8.44-hb1e8313_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/tk-8.6.10-hb0a8c7a_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/zeromq-4.3.4-h23ab428_0.conda
https://conda.anaconda.org/anaconda/osx-64/freetype-2.10.4-ha233b18_0.tar.bz2
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https://conda.anaconda.org/anaconda/osx-64/zstd-1.4.4-h1990bb4_3.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/fontconfig-2.13.0-h5d5b041_1.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/gettext-0.21.0-h7535e17_0.conda
https://conda.anaconda.org/anaconda/osx-64/libtiff-4.1.0-hcb84e12_1.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/sqlite-3.35.4-hce871da_0.conda
https://conda.anaconda.org/anaconda/osx-64/glib-2.56.2-hd9629dc_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/lcms2-2.11-h92f6f08_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/python-3.8.8-h88f2d9e_5.conda
https://repo.anaconda.com/pkgs/main/osx-64/qt-5.9.7-h468cd18_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/appnope-0.1.2-py38hecd8cb5_1001.conda
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https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.4-pyh9f0ad1d_0.tar.bz2
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https://conda.anaconda.org/conda-forge/noarch/dataclasses-0.8-pyhc8e2a94_1.tar.bz2
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https://repo.anaconda.com/pkgs/main/noarch/defusedxml-0.7.1-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/noarch/dictdiffer-0.8.0-py_0.conda
https://repo.anaconda.com/pkgs/main/noarch/dill-0.3.3-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/docutils-0.17.1-py38hecd8cb5_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/entrypoints-0.3-py38_0.conda
https://repo.anaconda.com/pkgs/main/noarch/et_xmlfile-1.0.1-py_1001.conda
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https://conda.anaconda.org/conda-forge/noarch/funcy-1.16-pyhd8ed1ab_0.tar.bz2
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https://repo.anaconda.com/pkgs/main/osx-64/psutil-5.8.0-py38h9ed2024_1.conda
https://repo.anaconda.com/pkgs/main/noarch/ptyprocess-0.7.0-pyhd3eb1b0_2.conda
https://conda.anaconda.org/conda-forge/noarch/pyasn1-0.4.8-py_0.tar.bz2
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https://conda.anaconda.org/conda-forge/noarch/tqdm-4.60.0-pyhd8ed1ab_0.tar.bz2
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https://conda.anaconda.org/conda-forge/osx-64/protobuf-3.16.0-py38ha048514_0.tar.bz2
https://repo.anaconda.com/pkgs/main/noarch/pygments-2.8.1-pyhd3eb1b0_0.conda
https://conda.anaconda.org/conda-forge/osx-64/srsly-2.4.1-py38ha048514_0.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/yarl-1.6.3-py38h5406a74_1.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/aiohttp-3.7.4-py38h96a0964_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/flask-2.0.0-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/google-resumable-media-1.2.0-pyhd3deb0d_0.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/googleapis-common-protos-1.53.0-py38h50d1736_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/graphviz-2.40.1-hefbbd9a_2.tar.bz2
https://repo.anaconda.com/pkgs/main/noarch/httpx-0.18.1-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/ipython-7.22.0-py38h01d92e1_0.conda
https://repo.anaconda.com/pkgs/main/noarch/jsonschema-3.2.0-py_2.conda
https://repo.anaconda.com/pkgs/main/noarch/jupyter_client-6.1.12-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/noarch/jupyterlab_pygments-0.1.2-py_0.conda
https://conda.anaconda.org/anaconda/noarch/nltk-3.5-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pyopenssl-20.0.1-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/flask-compress-1.9.0-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/google-auth-1.30.0-pyh44b312d_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/ipykernel-5.3.4-py38h5ca1d4c_0.conda
https://repo.anaconda.com/pkgs/main/noarch/nbformat-5.1.3-pyhd3eb1b0_0.conda
https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.4-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/botocore-1.20.72-pyhd8ed1ab_0.tar.bz2
https://repo.anaconda.com/pkgs/main/noarch/nbclient-0.5.3-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/noarch/qtconsole-5.0.3-pyhd3eb1b0_0.conda
https://conda.anaconda.org/conda-forge/noarch/requests-2.25.1-pyhd3deb0d_0.tar.bz2
https://repo.anaconda.com/pkgs/main/noarch/cachecontrol-0.12.6-py_0.conda
https://conda.anaconda.org/conda-forge/noarch/google-api-core-1.26.3-pyhd8ed1ab_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/nbconvert-6.0.7-py38_0.conda
https://conda.anaconda.org/conda-forge/noarch/s3transfer-0.4.2-pyhd8ed1ab_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/serverfiles-0.3.1-py38hecd8cb5_0.conda
https://conda.anaconda.org/conda-forge/noarch/boto3-1.17.72-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/google-cloud-core-1.5.0-pyhd3deb0d_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/notebook-6.3.0-py38hecd8cb5_0.conda
https://repo.anaconda.com/pkgs/main/noarch/orange-canvas-core-0.1.15-py_0.conda
https://conda.anaconda.org/conda-forge/noarch/google-cloud-storage-1.19.0-py_0.tar.bz2
https://repo.anaconda.com/pkgs/main/noarch/jupyterlab_server-1.2.0-py_0.conda
https://repo.anaconda.com/pkgs/main/noarch/jupyterlab-2.3.1-pyhd3eb1b0_0.conda
https://conda.anaconda.org/conda-forge/noarch/smart_open-2.2.1-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pathy-0.5.2-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/matplotlib-3.3.1-0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/matplotlib-base-3.3.1-py38h181983e_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/pandas-1.1.3-py38hb1e8313_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/dash-core-components-1.16.0-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/dash-html-components-1.1.3-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/dash-1.20.0-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/dash-table-4.11.3-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/cython-blis-0.7.4-py38ha1b04c9_0.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/numexpr-2.7.3-py38h1588c1c_0.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/thinc-8.0.3-py38he35c9cc_1.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/spacy-3.0.6-py38he35c9cc_0.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/xgboost-1.4.0-py38h50d1736_0.tar.bz2
https://repo.anaconda.com/pkgs/main/noarch/imageio-2.9.0-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/noarch/orange-widget-base-4.7.0-py_1.conda
https://repo.anaconda.com/pkgs/main/noarch/pyqtgraph-0.11.0-py_0.conda
https://repo.anaconda.com/pkgs/main/noarch/python-louvain-0.15-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/bokeh-2.3.2-py38hecd8cb5_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/bottleneck-1.3.2-py38hf1fa96c_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/distributed-2021.4.1-py38hecd8cb5_0.conda
https://repo.anaconda.com/pkgs/main/noarch/dask-2021.4.0-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/fast-histogram-0.9-py38he3068b8_0.conda
https://repo.anaconda.com/pkgs/main/noarch/mpl-scatter-density-0.7-py_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/h5py-2.10.0-py38h0601b69_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/mkl_fft-1.3.0-py38h4a7008c_2.conda
https://repo.anaconda.com/pkgs/main/osx-64/mkl_random-1.2.1-py38hb2f4e1b_2.conda
https://repo.anaconda.com/pkgs/main/osx-64/numpy-1.20.1-py38hd6e1bb9_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/numba-0.53.0-py38hb2f4e1b_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/pyerfa-1.7.3-py38h9ed2024_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/pywavelets-1.1.1-py38haf1e3a3_2.conda
https://repo.anaconda.com/pkgs/main/osx-64/scipy-1.6.2-py38hd5f7400_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/tifffile-2020.10.1-py38h0cf3a3e_2.conda
https://repo.anaconda.com/pkgs/main/osx-64/astropy-4.2.1-py38h9ed2024_1.conda
https://repo.anaconda.com/pkgs/main/noarch/baycomp-1.0.2-py_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/gensim-3.8.3-py38h23ab428_2.conda
https://conda.anaconda.org/conda-forge/noarch/pyldavis-3.3.1-pyhd8ed1ab_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/scikit-image-0.18.1-py38hb2f4e1b_0.conda
https://conda.anaconda.org/anaconda/osx-64/scikit-learn-0.23.2-py38h959d312_0.tar.bz2
https://conda.anaconda.org/anaconda/noarch/seaborn-0.11.0-py_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/glue-core-0.15.6-py38hecd8cb5_0.conda
https://conda.anaconda.org/conda-forge/osx-64/py-xgboost-1.4.0-py38h50d1736_0.tar.bz2
https://repo.anaconda.com/pkgs/main/noarch/pynndescent-0.5.2-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/noarch/glue-vispy-viewers-0.12.2-py_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/opentsne-0.3.11-py38h1de35cc_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/glueviz-1.0.0-0.conda
https://repo.anaconda.com/pkgs/main/osx-64/orange3-3.26.0-py38hb1e8313_0.conda

Please help. Thanks.

[dakinggg]

My guess is that something is not working on 20.0.4, but its a bit hard to know without digging further. The prime candidate is nmslib. Can you see if you are able to install and import nmslib separately from scispacy?

[dakinggg]

Great! That warning is not anything to worry about, just a warning from sklearn.