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mcollatz / EpiDope

Prediction of B-cell epitopes from amino acid sequences using deep neural networks.
MIT License
14 stars 10 forks source link

docker build -t epidope fails #8

Closed abrozzi closed 3 years ago

abrozzi commented 3 years ago

The command docker build -t epidope fails here:

Successfully built parsimonious word2number ftfy nltk overrides
Installing collected packages: jmespath, pytz, cymem, botocore, wasabi, srsly, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, s3transfer, Pygments, preshed, plac, murmurhash, itsdangerous, imagesize, docutils, click, blis, babel, alabaster, zope.interface, zope.event, wcwidth, toml, thinc, sphinx, sentencepiece, regex, py, pluggy, kiwisolver, iniconfig, greenlet, flask, cycler, boto3, attrs, word2number, unidecode, tensorboardX, sqlparse, spacy, responses, pytorch-transformers, pytorch-pretrained-bert, pytest, parsimonious, overrides, numpydoc, nltk, matplotlib, jsonpickle, gevent, ftfy, flask-cors, flaky, editdistance, conllu, allennlp
Killed
The command '/bin/sh -c pip install allennlp==0.9.0' returned a non-zero code: 137

This is the entire output:

Sending build context to Docker daemon  265.2kB
Step 1/9 : FROM continuumio/miniconda3
latest: Pulling from continuumio/miniconda3
852e50cd189d: Pull complete 
a6236801494d: Pull complete 
679c171d6942: Pull complete 
Digest: sha256:7838d0ce65783b0d944c19d193e2e6232196bada9e5f3762dc7a9f07dc271179
Status: Downloaded newer image for continuumio/miniconda3:latest
 ---> 52daacd3dd5d
Step 2/9 : ENV VERSION 0.2
 ---> Running in cb5a69df40be
Removing intermediate container cb5a69df40be
 ---> fd563ad1e44a
Step 3/9 : ENV TOOL epidope
 ---> Running in c935fc838b8e
Removing intermediate container c935fc838b8e
 ---> 5b5f301fdbbb
Step 4/9 : RUN apt update && apt install -y make g++ procps wget gzip && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 ---> Running in bd00146fdb54

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

Get:1 http://security.debian.org/debian-security buster/updates InRelease [65.4 kB]
Get:2 http://deb.debian.org/debian buster InRelease [122 kB]
Get:3 http://deb.debian.org/debian buster-updates InRelease [51.9 kB]
Get:4 http://deb.debian.org/debian buster/main amd64 Packages [7907 kB]
Get:5 http://security.debian.org/debian-security buster/updates/main amd64 Packages [268 kB]
Get:6 http://deb.debian.org/debian buster-updates/main amd64 Packages.diff/Index [5656 B]
Get:7 http://deb.debian.org/debian buster-updates/main amd64 Packages 2020-12-24-1401.30.pdiff [286 B]
Get:8 http://deb.debian.org/debian buster-updates/main amd64 Packages 2021-01-29-2000.47.pdiff [408 B]
Get:9 http://deb.debian.org/debian buster-updates/main amd64 Packages 2021-02-07-1359.56.pdiff [2302 B]
Get:9 http://deb.debian.org/debian buster-updates/main amd64 Packages 2021-02-07-1359.56.pdiff [2302 B]
Fetched 8422 kB in 3s (2875 kB/s)
Reading package lists...
Building dependency tree...
Reading state information...
19 packages can be upgraded. Run 'apt list --upgradable' to see them.

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

Reading package lists...
Building dependency tree...
Reading state information...
gzip is already the newest version (1.9-3).
gzip set to manually installed.
wget is already the newest version (1.20.1-1.1).
The following additional packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-8 g++-8 gcc gcc-8
  libasan5 libatomic1 libbinutils libc-dev-bin libc6-dev libcc1-0 libgcc-8-dev
  libgomp1 libgpm2 libisl19 libitm1 liblsan0 libmpc3 libmpfr6 libmpx2
  libncurses6 libprocps7 libquadmath0 libstdc++-8-dev libtsan0 libubsan1
  linux-libc-dev manpages manpages-dev psmisc
Suggested packages:
  binutils-doc cpp-doc gcc-8-locales g++-multilib g++-8-multilib gcc-8-doc
  libstdc++6-8-dbg gcc-multilib autoconf automake libtool flex bison gdb
  gcc-doc gcc-8-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
  libasan5-dbg liblsan0-dbg libtsan0-dbg libubsan1-dbg libmpx2-dbg
  libquadmath0-dbg glibc-doc gpm libstdc++-8-doc make-doc man-browser
The following NEW packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-8 g++ g++-8 gcc
  gcc-8 libasan5 libatomic1 libbinutils libc-dev-bin libc6-dev libcc1-0
  libgcc-8-dev libgomp1 libgpm2 libisl19 libitm1 liblsan0 libmpc3 libmpfr6
  libmpx2 libncurses6 libprocps7 libquadmath0 libstdc++-8-dev libtsan0
  libubsan1 linux-libc-dev make manpages manpages-dev procps psmisc
0 upgraded, 36 newly installed, 0 to remove and 19 not upgraded.
Need to get 47.9 MB of archives.
After this operation, 184 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB]
Get:2 http://deb.debian.org/debian buster/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB]
Get:3 http://deb.debian.org/debian buster/main amd64 procps amd64 2:3.3.15-2 [259 kB]
Get:4 http://deb.debian.org/debian buster/main amd64 manpages all 4.16-2 [1295 kB]
Get:5 http://deb.debian.org/debian buster/main amd64 binutils-common amd64 2.31.1-16 [2073 kB]
Get:6 http://deb.debian.org/debian buster/main amd64 libbinutils amd64 2.31.1-16 [478 kB]
Get:7 http://deb.debian.org/debian buster/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-16 [1823 kB]
Get:8 http://deb.debian.org/debian buster/main amd64 binutils amd64 2.31.1-16 [56.8 kB]
Get:9 http://deb.debian.org/debian buster/main amd64 libisl19 amd64 0.20-2 [587 kB]
Get:10 http://deb.debian.org/debian buster/main amd64 libmpfr6 amd64 4.0.2-1 [775 kB]
Get:11 http://deb.debian.org/debian buster/main amd64 libmpc3 amd64 1.1.0-1 [41.3 kB]
Get:12 http://deb.debian.org/debian buster/main amd64 cpp-8 amd64 8.3.0-6 [8914 kB]
Get:13 http://deb.debian.org/debian buster/main amd64 cpp amd64 4:8.3.0-1 [19.4 kB]
Get:14 http://deb.debian.org/debian buster/main amd64 libcc1-0 amd64 8.3.0-6 [46.6 kB]
Get:15 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB]
Get:16 http://deb.debian.org/debian buster/main amd64 libitm1 amd64 8.3.0-6 [27.7 kB]
Get:17 http://deb.debian.org/debian buster/main amd64 libatomic1 amd64 8.3.0-6 [9032 B]
Get:18 http://deb.debian.org/debian buster/main amd64 libasan5 amd64 8.3.0-6 [362 kB]
Get:19 http://deb.debian.org/debian buster/main amd64 liblsan0 amd64 8.3.0-6 [131 kB]
Get:20 http://deb.debian.org/debian buster/main amd64 libtsan0 amd64 8.3.0-6 [283 kB]
Get:21 http://deb.debian.org/debian buster/main amd64 libubsan1 amd64 8.3.0-6 [120 kB]
Get:22 http://deb.debian.org/debian buster/main amd64 libmpx2 amd64 8.3.0-6 [11.4 kB]
Get:23 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB]
Get:24 http://deb.debian.org/debian buster/main amd64 libgcc-8-dev amd64 8.3.0-6 [2298 kB]
Get:25 http://deb.debian.org/debian buster/main amd64 gcc-8 amd64 8.3.0-6 [9452 kB]
Get:26 http://deb.debian.org/debian buster/main amd64 gcc amd64 4:8.3.0-1 [5196 B]
Get:27 http://deb.debian.org/debian buster/main amd64 libc-dev-bin amd64 2.28-10 [275 kB]
Get:28 http://deb.debian.org/debian buster/main amd64 linux-libc-dev amd64 4.19.171-2 [1430 kB]
Get:29 http://deb.debian.org/debian buster/main amd64 libc6-dev amd64 2.28-10 [2691 kB]
Get:30 http://deb.debian.org/debian buster/main amd64 libstdc++-8-dev amd64 8.3.0-6 [1532 kB]
Get:31 http://deb.debian.org/debian buster/main amd64 g++-8 amd64 8.3.0-6 [9752 kB]
Get:32 http://deb.debian.org/debian buster/main amd64 g++ amd64 4:8.3.0-1 [1644 B]
Get:33 http://deb.debian.org/debian buster/main amd64 libgpm2 amd64 1.20.7-5 [35.1 kB]
Get:34 http://deb.debian.org/debian buster/main amd64 make amd64 4.2.1-1.2 [341 kB]
Get:35 http://deb.debian.org/debian buster/main amd64 manpages-dev all 4.16-2 [2232 kB]
Get:36 http://deb.debian.org/debian buster/main amd64 psmisc amd64 23.2-1 [126 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 47.9 MB in 11s (4329 kB/s)
Selecting previously unselected package libncurses6:amd64.
(Reading database ... 12571 files and directories currently installed.)
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Setting up libgpm2:amd64 (1.20.7-5) ...
Setting up psmisc (23.2-1) ...
Setting up manpages (4.16-2) ...
Setting up libprocps7:amd64 (2:3.3.15-2) ...
Setting up binutils-common:amd64 (2.31.1-16) ...
Setting up linux-libc-dev:amd64 (4.19.171-2) ...
Setting up libgomp1:amd64 (8.3.0-6) ...
Setting up libasan5:amd64 (8.3.0-6) ...
Setting up make (4.2.1-1.2) ...
Setting up libmpfr6:amd64 (4.0.2-1) ...
Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ...
Setting up libquadmath0:amd64 (8.3.0-6) ...
Setting up libmpc3:amd64 (1.1.0-1) ...
Setting up libatomic1:amd64 (8.3.0-6) ...
Setting up libmpx2:amd64 (8.3.0-6) ...
Setting up libubsan1:amd64 (8.3.0-6) ...
Setting up libisl19:amd64 (0.20-2) ...
Setting up procps (2:3.3.15-2) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/w.1.gz because associated file /usr/share/man/man1/w.procps.1.gz (of link group w) doesn't exist
Setting up libbinutils:amd64 (2.31.1-16) ...
Setting up cpp-8 (8.3.0-6) ...
Setting up libc-dev-bin (2.28-10) ...
Setting up libcc1-0:amd64 (8.3.0-6) ...
Setting up liblsan0:amd64 (8.3.0-6) ...
Setting up libitm1:amd64 (8.3.0-6) ...
Setting up binutils-x86-64-linux-gnu (2.31.1-16) ...
Setting up libtsan0:amd64 (8.3.0-6) ...
Setting up manpages-dev (4.16-2) ...
Setting up binutils (2.31.1-16) ...
Setting up libgcc-8-dev:amd64 (8.3.0-6) ...
Setting up cpp (4:8.3.0-1) ...
Setting up libc6-dev:amd64 (2.28-10) ...
Setting up libstdc++-8-dev:amd64 (8.3.0-6) ...
Setting up gcc-8 (8.3.0-6) ...
Setting up gcc (4:8.3.0-1) ...
Setting up g++-8 (8.3.0-6) ...
Setting up g++ (4:8.3.0-1) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Processing triggers for libc-bin (2.28-10) ...
Removing intermediate container bd00146fdb54
 ---> 13be42c36784
Step 5/9 : RUN conda config --add channels conda-forge &&     conda config --add channels flomock &&     conda config --add channels pytorch &&     conda config --add channels default
 ---> Running in d85c3e6f80d2
Removing intermediate container d85c3e6f80d2
 ---> 4535b30395e6
Step 6/9 : RUN conda install -y python=3.7 pip $TOOL=$VERSION h5py=2.10 jsonnet && conda clean -a
 ---> Running in 54babd0f1a2b
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - epidope=0.2
    - h5py=2.10
    - jsonnet
    - pip
    - python=3.7

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    absl-py-0.11.0             |   py37h89c1867_0         168 KB  conda-forge
    astor-0.8.1                |     pyh9f0ad1d_0          25 KB  conda-forge
    blas-2.14                  |         openblas          10 KB  conda-forge
    bokeh-1.4.0                |   py37hc8dfbb8_1        13.5 MB  conda-forge
    brotlipy-0.7.0             |py37hb5d75c8_1001         346 KB  conda-forge
    c-ares-1.17.1              |       h36c2ea0_0         111 KB  conda-forge
    ca-certificates-2020.12.5  |       ha878542_0         137 KB  conda-forge
    certifi-2020.12.5          |   py37h89c1867_1         143 KB  conda-forge
    cffi-1.14.4                |   py37h11fe52a_0         224 KB  conda-forge
    chardet-3.0.4              |py37he5f6b98_1008         170 KB  conda-forge
    conda-4.9.2                |   py37h89c1867_0         3.0 MB  conda-forge
    conda-package-handling-1.7.2|   py37hb5d75c8_0         915 KB  conda-forge
    cryptography-3.2.1         |   py37hc72a4ac_0         623 KB  conda-forge
    cudatoolkit-10.1.243       |       h6bb024c_0       347.4 MB
    epidope-0.2                |            py_24       341.2 MB  flomock
    freetype-2.10.4            |       h7ca028e_0         912 KB  conda-forge
    gast-0.4.0                 |     pyh9f0ad1d_0          12 KB  conda-forge
    giflib-5.2.1               |       h36c2ea0_2          77 KB  conda-forge
    grpcio-1.33.2              |   py37haffed2e_2         1.8 MB  conda-forge
    h5py-2.10.0                |nompi_py37hf7afa78_105         1.1 MB  conda-forge
    hdf5-1.10.6                |nompi_h3c11f04_101         3.0 MB  conda-forge
    idna-2.10                  |             py_0          50 KB
    importlib-metadata-3.7.2   |   py37h89c1867_0          24 KB  conda-forge
    intel-openmp-2020.2        |              254         786 KB
    jinja2-2.11.3              |     pyh44b312d_0          93 KB  conda-forge
    joblib-1.0.1               |     pyhd8ed1ab_0         206 KB  conda-forge
    jpeg-9d                    |       h36c2ea0_0         264 KB  conda-forge
    jsonnet-0.17.0             |   py37h745909e_0         327 KB  conda-forge
    keras-2.3.1                |           py37_0         591 KB  conda-forge
    keras-applications-1.0.8   |             py_1          30 KB  conda-forge
    keras-preprocessing-1.1.2  |     pyhd8ed1ab_0          34 KB  conda-forge
    lcms2-2.11                 |       hcbb858e_1         434 KB  conda-forge
    libblas-3.8.0              |      14_openblas          10 KB  conda-forge
    libcblas-3.8.0             |      14_openblas          10 KB  conda-forge
    libffi-3.2.1               |    he1b5a44_1007          47 KB  conda-forge
    libgfortran-ng-7.5.0       |      h14aa051_18          22 KB  conda-forge
    libgfortran4-7.5.0         |      h14aa051_18         1.3 MB  conda-forge
    libgpuarray-0.7.6          |    h14c3975_1003         263 KB  conda-forge
    liblapack-3.8.0            |      14_openblas          10 KB  conda-forge
    liblapacke-3.8.0           |      14_openblas          10 KB  conda-forge
    libopenblas-0.3.7          |       h5ec1e0e_6         7.6 MB  conda-forge
    libpng-1.6.37              |       h21135ba_2         306 KB  conda-forge
    libprotobuf-3.13.0.1       |       h8b12597_0         2.3 MB  conda-forge
    libtiff-4.1.0              |       hc3755c2_3         568 KB  conda-forge
    libwebp-1.0.2              |       h56121f0_5         938 KB  conda-forge
    lz4-c-1.9.2                |       he1b5a44_3         203 KB  conda-forge
    mako-1.1.4                 |     pyh44b312d_0          58 KB  conda-forge
    markdown-3.3.4             |     pyhd8ed1ab_0          67 KB  conda-forge
    markupsafe-1.1.1           |   py37hb5d75c8_2          27 KB  conda-forge
    mkl-2020.2                 |              256       138.3 MB
    mock-4.0.3                 |   py37h89c1867_1          51 KB  conda-forge
    ninja-1.10.1               |       hfc4b9b4_2         1.9 MB  conda-forge
    numpy-1.17.4               |   py37hd5be1e1_0           4 KB
    numpy-base-1.17.4          |   py37h2f8d375_0         4.1 MB
    olefile-0.46               |     pyh9f0ad1d_1          32 KB  conda-forge
    openssl-1.1.1h             |       h516909a_0         2.1 MB  conda-forge
    packaging-20.9             |     pyh44b312d_0          35 KB  conda-forge
    pillow-8.0.1               |   py37h63a5d19_0         689 KB  conda-forge
    pip-21.0.1                 |     pyhd8ed1ab_0         1.1 MB  conda-forge
    protobuf-3.13.0.1          |   py37h745909e_1         704 KB  conda-forge
    pycosat-0.6.3              |py37hb5d75c8_1005         107 KB  conda-forge
    pycparser-2.20             |             py_2          94 KB
    pygpu-0.7.6                |py37h161383b_1002         654 KB  conda-forge
    pyopenssl-19.1.0           |     pyhd3eb1b0_1          52 KB
    pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  conda-forge
    pysocks-1.7.1              |   py37h89c1867_3          27 KB  conda-forge
    python-3.7.6               |cpython_h8356626_6        53.0 MB  conda-forge
    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge
    python_abi-3.7             |          1_cp37m           4 KB  conda-forge
    pytorch-1.3.1              |py3.7_cuda10.1.243_cudnn7.6.3_0       428.0 MB  pytorch
    pyyaml-5.3.1               |   py37hb5d75c8_1         185 KB  conda-forge
    requests-2.24.0            |             py_0          56 KB
    ruamel_yaml-0.15.80        |py37hb5d75c8_1003         252 KB  conda-forge
    scikit-learn-0.22          |   py37hcdab131_1         7.1 MB  conda-forge
    scipy-1.5.3                |   py37h8911b10_0        18.5 MB  conda-forge
    setuptools-49.6.0          |   py37h89c1867_3         947 KB  conda-forge
    six-1.15.0                 |     pyh9f0ad1d_0          14 KB  conda-forge
    tensorboard-1.13.1         |           py37_0         3.3 MB  conda-forge
    tensorflow-1.13.1          |   py37h90a7d86_1        75.5 MB  conda-forge
    tensorflow-estimator-1.13.0|             py_0         181 KB
    termcolor-1.1.0            |             py_2           6 KB  conda-forge
    theano-1.0.3               |   py37hfc679d8_1         3.6 MB  conda-forge
    toolchain-2.4.0            |                0          14 KB
    toolchain_c_linux-64-2.4.0 |                0          13 KB
    toolchain_cxx_linux-64-2.4.0|                0          13 KB
    tornado-6.1                |   py37h4abf009_0         645 KB  conda-forge
    tqdm-4.51.0                |     pyhd3eb1b0_0          66 KB
    typing_extensions-3.7.4.3  |             py_0          25 KB  conda-forge
    urllib3-1.25.11            |             py_0          99 KB
    werkzeug-1.0.1             |     pyh9f0ad1d_0         239 KB  conda-forge
    wheel-0.35.1               |     pyhd3eb1b0_0          38 KB
    zipp-3.4.1                 |     pyhd8ed1ab_0          11 KB  conda-forge
    zstd-1.4.5                 |       h6597ccf_2         712 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        1.44 GB

The following NEW packages will be INSTALLED:

  absl-py            conda-forge/linux-64::absl-py-0.11.0-py37h89c1867_0
  astor              conda-forge/noarch::astor-0.8.1-pyh9f0ad1d_0
  blas               conda-forge/linux-64::blas-2.14-openblas
  bokeh              conda-forge/linux-64::bokeh-1.4.0-py37hc8dfbb8_1
  c-ares             conda-forge/linux-64::c-ares-1.17.1-h36c2ea0_0
  cudatoolkit        pkgs/main/linux-64::cudatoolkit-10.1.243-h6bb024c_0
  epidope            flomock/noarch::epidope-0.2-py_24
  freetype           conda-forge/linux-64::freetype-2.10.4-h7ca028e_0
  gast               conda-forge/noarch::gast-0.4.0-pyh9f0ad1d_0
  giflib             conda-forge/linux-64::giflib-5.2.1-h36c2ea0_2
  grpcio             conda-forge/linux-64::grpcio-1.33.2-py37haffed2e_2
  h5py               conda-forge/linux-64::h5py-2.10.0-nompi_py37hf7afa78_105
  hdf5               conda-forge/linux-64::hdf5-1.10.6-nompi_h3c11f04_101
  importlib-metadata conda-forge/linux-64::importlib-metadata-3.7.2-py37h89c1867_0
  intel-openmp       pkgs/main/linux-64::intel-openmp-2020.2-254
  jinja2             conda-forge/noarch::jinja2-2.11.3-pyh44b312d_0
  joblib             conda-forge/noarch::joblib-1.0.1-pyhd8ed1ab_0
  jpeg               conda-forge/linux-64::jpeg-9d-h36c2ea0_0
  jsonnet            conda-forge/linux-64::jsonnet-0.17.0-py37h745909e_0
  keras              conda-forge/linux-64::keras-2.3.1-py37_0
  keras-applications conda-forge/noarch::keras-applications-1.0.8-py_1
  keras-preprocessi~ conda-forge/noarch::keras-preprocessing-1.1.2-pyhd8ed1ab_0
  lcms2              conda-forge/linux-64::lcms2-2.11-hcbb858e_1
  libblas            conda-forge/linux-64::libblas-3.8.0-14_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-14_openblas
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-h14aa051_18
  libgfortran4       conda-forge/linux-64::libgfortran4-7.5.0-h14aa051_18
  libgpuarray        conda-forge/linux-64::libgpuarray-0.7.6-h14c3975_1003
  liblapack          conda-forge/linux-64::liblapack-3.8.0-14_openblas
  liblapacke         conda-forge/linux-64::liblapacke-3.8.0-14_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.7-h5ec1e0e_6
  libpng             conda-forge/linux-64::libpng-1.6.37-h21135ba_2
  libprotobuf        conda-forge/linux-64::libprotobuf-3.13.0.1-h8b12597_0
  libtiff            conda-forge/linux-64::libtiff-4.1.0-hc3755c2_3
  libwebp            conda-forge/linux-64::libwebp-1.0.2-h56121f0_5
  lz4-c              conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_3
  mako               conda-forge/noarch::mako-1.1.4-pyh44b312d_0
  markdown           conda-forge/noarch::markdown-3.3.4-pyhd8ed1ab_0
  markupsafe         conda-forge/linux-64::markupsafe-1.1.1-py37hb5d75c8_2
  mkl                pkgs/main/linux-64::mkl-2020.2-256
  mock               conda-forge/linux-64::mock-4.0.3-py37h89c1867_1
  ninja              conda-forge/linux-64::ninja-1.10.1-hfc4b9b4_2
  numpy              pkgs/main/linux-64::numpy-1.17.4-py37hd5be1e1_0
  numpy-base         pkgs/main/linux-64::numpy-base-1.17.4-py37h2f8d375_0
  olefile            conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
  packaging          conda-forge/noarch::packaging-20.9-pyh44b312d_0
  pillow             conda-forge/linux-64::pillow-8.0.1-py37h63a5d19_0
  protobuf           conda-forge/linux-64::protobuf-3.13.0.1-py37h745909e_1
  pygpu              conda-forge/linux-64::pygpu-0.7.6-py37h161383b_1002
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  pytorch            pytorch/linux-64::pytorch-1.3.1-py3.7_cuda10.1.243_cudnn7.6.3_0
  pyyaml             conda-forge/linux-64::pyyaml-5.3.1-py37hb5d75c8_1
  scikit-learn       conda-forge/linux-64::scikit-learn-0.22-py37hcdab131_1
  scipy              conda-forge/linux-64::scipy-1.5.3-py37h8911b10_0
  tensorboard        conda-forge/linux-64::tensorboard-1.13.1-py37_0
  tensorflow         conda-forge/linux-64::tensorflow-1.13.1-py37h90a7d86_1
  tensorflow-estima~ pkgs/main/noarch::tensorflow-estimator-1.13.0-py_0
  termcolor          conda-forge/noarch::termcolor-1.1.0-py_2
  theano             conda-forge/linux-64::theano-1.0.3-py37hfc679d8_1
  toolchain          pkgs/main/linux-64::toolchain-2.4.0-0
  toolchain_c_linux~ pkgs/main/linux-64::toolchain_c_linux-64-2.4.0-0
  toolchain_cxx_lin~ pkgs/main/linux-64::toolchain_cxx_linux-64-2.4.0-0
  tornado            conda-forge/linux-64::tornado-6.1-py37h4abf009_0
  typing_extensions  conda-forge/noarch::typing_extensions-3.7.4.3-py_0
  werkzeug           conda-forge/noarch::werkzeug-1.0.1-pyh9f0ad1d_0
  zipp               conda-forge/noarch::zipp-3.4.1-pyhd8ed1ab_0
  zstd               conda-forge/linux-64::zstd-1.4.5-h6597ccf_2

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2020.10.14~ --> conda-forge::ca-certificates-2020.12.5-ha878542_0
  certifi            pkgs/main/noarch::certifi-2020.6.20-p~ --> conda-forge/linux-64::certifi-2020.12.5-py37h89c1867_1
  cffi                pkgs/main::cffi-1.14.3-py38h261ae71_2 --> conda-forge::cffi-1.14.4-py37h11fe52a_0
  chardet            pkgs/main::chardet-3.0.4-py38h06a4308~ --> conda-forge::chardet-3.0.4-py37he5f6b98_1008
  pip                pkgs/main/linux-64::pip-20.2.4-py38h0~ --> conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  pycosat            pkgs/main::pycosat-0.6.3-py38h7b6447c~ --> conda-forge::pycosat-0.6.3-py37hb5d75c8_1005
  pysocks            pkgs/main::pysocks-1.7.1-py38h06a4308~ --> conda-forge::pysocks-1.7.1-py37h89c1867_3

The following packages will be SUPERSEDED by a higher-priority channel:

  brotlipy           pkgs/main::brotlipy-0.7.0-py38h27cfd2~ --> conda-forge::brotlipy-0.7.0-py37hb5d75c8_1001
  conda               pkgs/main::conda-4.9.2-py38h06a4308_0 --> conda-forge::conda-4.9.2-py37h89c1867_0
  conda-package-han~ pkgs/main::conda-package-handling-1.7~ --> conda-forge::conda-package-handling-1.7.2-py37hb5d75c8_0
  cryptography       pkgs/main::cryptography-3.2.1-py38h3c~ --> conda-forge::cryptography-3.2.1-py37hc72a4ac_0
  libffi                   pkgs/main::libffi-3.3-he6710b0_2 --> conda-forge::libffi-3.2.1-he1b5a44_1007
  openssl              pkgs/main::openssl-1.1.1h-h7b6447c_0 --> conda-forge::openssl-1.1.1h-h516909a_0
  python                 pkgs/main::python-3.8.5-h7579374_1 --> conda-forge::python-3.7.6-cpython_h8356626_6
  ruamel_yaml        pkgs/main::ruamel_yaml-0.15.87-py38h7~ --> conda-forge::ruamel_yaml-0.15.80-py37hb5d75c8_1003
  setuptools         pkgs/main::setuptools-50.3.1-py38h06a~ --> conda-forge::setuptools-49.6.0-py37h89c1867_3
  six                pkgs/main/linux-64::six-1.15.0-py38h0~ --> conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0

Downloading and Extracting Packages
astor-0.8.1          | 25 KB     | ########## | 100% 
joblib-1.0.1         | 206 KB    | ########## | 100% 
mock-4.0.3           | 51 KB     | ########## | 100% 
ca-certificates-2020 | 137 KB    | ########## | 100% 
pygpu-0.7.6          | 654 KB    | ########## | 100% 
pip-21.0.1           | 1.1 MB    | ########## | 100% 
tornado-6.1          | 645 KB    | ########## | 100% 
tqdm-4.51.0          | 66 KB     | ########## | 100% 
werkzeug-1.0.1       | 239 KB    | ########## | 100% 
pyyaml-5.3.1         | 185 KB    | ########## | 100% 
setuptools-49.6.0    | 947 KB    | ########## | 100% 
brotlipy-0.7.0       | 346 KB    | ########## | 100% 
toolchain_cxx_linux- | 13 KB     | ########## | 100% 
zipp-3.4.1           | 11 KB     | ########## | 100% 
numpy-1.17.4         | 4 KB      | ########## | 100% 
gast-0.4.0           | 12 KB     | ########## | 100% 
lcms2-2.11           | 434 KB    | ########## | 100% 
libtiff-4.1.0        | 568 KB    | ########## | 100% 
conda-package-handli | 915 KB    | ########## | 100% 
numpy-base-1.17.4    | 4.1 MB    | ########## | 100% 
keras-2.3.1          | 591 KB    | ########## | 100% 
keras-applications-1 | 30 KB     | ########## | 100% 
packaging-20.9       | 35 KB     | ########## | 100% 
pyparsing-2.4.7      | 60 KB     | ########## | 100% 
toolchain-2.4.0      | 14 KB     | ########## | 100% 
chardet-3.0.4        | 170 KB    | ########## | 100% 
liblapack-3.8.0      | 10 KB     | ########## | 100% 
tensorflow-1.13.1    | 75.5 MB   | ########## | 100% 
tensorflow-estimator | 181 KB    | ########## | 100% 
pillow-8.0.1         | 689 KB    | ########## | 100% 
six-1.15.0           | 14 KB     | ########## | 100% 
pysocks-1.7.1        | 27 KB     | ########## | 100% 
keras-preprocessing- | 34 KB     | ########## | 100% 
theano-1.0.3         | 3.6 MB    | ########## | 100% 
pyopenssl-19.1.0     | 52 KB     | ########## | 100% 
libgfortran4-7.5.0   | 1.3 MB    | ########## | 100% 
intel-openmp-2020.2  | 786 KB    | ########## | 100% 
h5py-2.10.0          | 1.1 MB    | ########## | 100% 
bokeh-1.4.0          | 13.5 MB   | ########## | 100% 
pycparser-2.20       | 94 KB     | ########## | 100% 
openssl-1.1.1h       | 2.1 MB    | ########## | 100% 
certifi-2020.12.5    | 143 KB    | ########## | 100% 
lz4-c-1.9.2          | 203 KB    | ########## | 100% 
libopenblas-0.3.7    | 7.6 MB    | ########## | 100% 
markupsafe-1.1.1     | 27 KB     | ########## | 100% 
absl-py-0.11.0       | 168 KB    | ########## | 100% 
ruamel_yaml-0.15.80  | 252 KB    | ########## | 100% 
pytorch-1.3.1        | 428.0 MB  | ########## | 100% 
zstd-1.4.5           | 712 KB    | ########## | 100% 
libgpuarray-0.7.6    | 263 KB    | ########## | 100% 
termcolor-1.1.0      | 6 KB      | ########## | 100% 
scipy-1.5.3          | 18.5 MB   | ########## | 100% 
cryptography-3.2.1   | 623 KB    | ########## | 100% 
requests-2.24.0      | 56 KB     | ########## | 100% 
libgfortran-ng-7.5.0 | 22 KB     | ########## | 100% 
cudatoolkit-10.1.243 | 347.4 MB  | ########## | 100% 
wheel-0.35.1         | 38 KB     | ########## | 100% 
mako-1.1.4           | 58 KB     | ########## | 100% 
typing_extensions-3. | 25 KB     | ########## | 100% 
conda-4.9.2          | 3.0 MB    | ########## | 100% 
pycosat-0.6.3        | 107 KB    | ########## | 100% 
tensorboard-1.13.1   | 3.3 MB    | ########## | 100% 
toolchain_c_linux-64 | 13 KB     | ########## | 100% 
cffi-1.14.4          | 224 KB    | ########## | 100% 
jsonnet-0.17.0       | 327 KB    | ########## | 100% 
jpeg-9d              | 264 KB    | ########## | 100% 
python-dateutil-2.8. | 220 KB    | ########## | 100% 
scikit-learn-0.22    | 7.1 MB    | ########## | 100% 
libcblas-3.8.0       | 10 KB     | ########## | 100% 
importlib-metadata-3 | 24 KB     | ########## | 100% 
libpng-1.6.37        | 306 KB    | ########## | 100% 
urllib3-1.25.11      | 99 KB     | ########## | 100% 
jinja2-2.11.3        | 93 KB     | ########## | 100% 
idna-2.10            | 50 KB     | ########## | 100% 
giflib-5.2.1         | 77 KB     | ########## | 100% 
python_abi-3.7       | 4 KB      | ########## | 100% 
mkl-2020.2           | 138.3 MB  | ########## | 100% 
hdf5-1.10.6          | 3.0 MB    | ########## | 100% 
python-3.7.6         | 53.0 MB   | ########## | 100% 
liblapacke-3.8.0     | 10 KB     | ########## | 100% 
protobuf-3.13.0.1    | 704 KB    | ########## | 100% 
c-ares-1.17.1        | 111 KB    | ########## | 100% 
libwebp-1.0.2        | 938 KB    | ########## | 100% 
libblas-3.8.0        | 10 KB     | ########## | 100% 
markdown-3.3.4       | 67 KB     | ########## | 100% 
epidope-0.2          | 341.2 MB  | ########## | 100% 
libffi-3.2.1         | 47 KB     | ########## | 100% 
olefile-0.46         | 32 KB     | ########## | 100% 
libprotobuf-3.13.0.1 | 2.3 MB    | ########## | 100% 
freetype-2.10.4      | 912 KB    | ########## | 100% 
ninja-1.10.1         | 1.9 MB    | ########## | 100% 
blas-2.14            | 10 KB     | ########## | 100% 
grpcio-1.33.2        | 1.8 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Cache location: /opt/conda/pkgs
Will remove the following tarballs:

/opt/conda/pkgs
---------------
scipy-1.5.3-py37h8911b10_0.tar.bz2          18.5 MB
bokeh-1.4.0-py37hc8dfbb8_1.tar.bz2          13.5 MB
typing_extensions-3.7.4.3-py_0.tar.bz2        25 KB
conda-4.9.2-py37h89c1867_0.tar.bz2           3.0 MB
python-3.7.6-cpython_h8356626_6.tar.bz2     53.0 MB
toolchain_c_linux-64-2.4.0-0.conda            13 KB
requests-2.24.0-py_0.conda                    56 KB
lcms2-2.11-hcbb858e_1.tar.bz2                434 KB
wheel-0.35.1-pyhd3eb1b0_0.conda               38 KB
absl-py-0.11.0-py37h89c1867_0.tar.bz2        168 KB
gast-0.4.0-pyh9f0ad1d_0.tar.bz2               12 KB
libgpuarray-0.7.6-h14c3975_1003.tar.bz2      263 KB
pyparsing-2.4.7-pyh9f0ad1d_0.tar.bz2          60 KB
liblapacke-3.8.0-14_openblas.tar.bz2          10 KB
werkzeug-1.0.1-pyh9f0ad1d_0.tar.bz2          239 KB
mkl-2020.2-256.conda                       138.3 MB
jsonnet-0.17.0-py37h745909e_0.tar.bz2        327 KB
theano-1.0.3-py37hfc679d8_1.tar.bz2          3.6 MB
openssl-1.1.1h-h516909a_0.tar.bz2            2.1 MB
tqdm-4.51.0-pyhd3eb1b0_0.conda                66 KB
mako-1.1.4-pyh44b312d_0.tar.bz2               58 KB
chardet-3.0.4-py37he5f6b98_1008.tar.bz2      170 KB
six-1.15.0-pyh9f0ad1d_0.tar.bz2               14 KB
pycparser-2.20-py_2.conda                     94 KB
ruamel_yaml-0.15.80-py37hb5d75c8_1003.tar.bz2     252 KB
libwebp-1.0.2-h56121f0_5.tar.bz2             938 KB
astor-0.8.1-pyh9f0ad1d_0.tar.bz2              25 KB
pysocks-1.7.1-py37h89c1867_3.tar.bz2          27 KB
c-ares-1.17.1-h36c2ea0_0.tar.bz2             111 KB
brotlipy-0.7.0-py37hb5d75c8_1001.tar.bz2     346 KB
intel-openmp-2020.2-254.conda                786 KB
libcblas-3.8.0-14_openblas.tar.bz2            10 KB
liblapack-3.8.0-14_openblas.tar.bz2           10 KB
giflib-5.2.1-h36c2ea0_2.tar.bz2               77 KB
h5py-2.10.0-nompi_py37hf7afa78_105.tar.bz2     1.1 MB
toolchain-2.4.0-0.conda                       14 KB
markupsafe-1.1.1-py37hb5d75c8_2.tar.bz2       27 KB
olefile-0.46-pyh9f0ad1d_1.tar.bz2             32 KB
zstd-1.4.5-h6597ccf_2.tar.bz2                712 KB
mock-4.0.3-py37h89c1867_1.tar.bz2             51 KB
protobuf-3.13.0.1-py37h745909e_1.tar.bz2     704 KB
numpy-1.17.4-py37hd5be1e1_0.conda              4 KB
freetype-2.10.4-h7ca028e_0.tar.bz2           912 KB
tensorflow-estimator-1.13.0-py_0.conda       181 KB
epidope-0.2-py_24.tar.bz2                  341.2 MB
libopenblas-0.3.7-h5ec1e0e_6.tar.bz2         7.6 MB
ca-certificates-2020.12.5-ha878542_0.tar.bz2     137 KB
pycosat-0.6.3-py37hb5d75c8_1005.tar.bz2      107 KB
setuptools-49.6.0-py37h89c1867_3.tar.bz2     947 KB
importlib-metadata-3.7.2-py37h89c1867_0.tar.bz2      24 KB
libffi-3.2.1-he1b5a44_1007.tar.bz2            47 KB
toolchain_cxx_linux-64-2.4.0-0.conda          13 KB
pygpu-0.7.6-py37h161383b_1002.tar.bz2        654 KB
pip-21.0.1-pyhd8ed1ab_0.tar.bz2              1.1 MB
termcolor-1.1.0-py_2.tar.bz2                   6 KB
cffi-1.14.4-py37h11fe52a_0.tar.bz2           224 KB
packaging-20.9-pyh44b312d_0.tar.bz2           35 KB
ninja-1.10.1-hfc4b9b4_2.tar.bz2              1.9 MB
pyopenssl-19.1.0-pyhd3eb1b0_1.conda           52 KB
joblib-1.0.1-pyhd8ed1ab_0.tar.bz2            206 KB
libblas-3.8.0-14_openblas.tar.bz2             10 KB
grpcio-1.33.2-py37haffed2e_2.tar.bz2         1.8 MB
markdown-3.3.4-pyhd8ed1ab_0.tar.bz2           67 KB
pyyaml-5.3.1-py37hb5d75c8_1.tar.bz2          185 KB
idna-2.10-py_0.conda                          50 KB
tensorboard-1.13.1-py37_0.tar.bz2            3.3 MB
libgfortran4-7.5.0-h14aa051_18.tar.bz2       1.3 MB
cudatoolkit-10.1.243-h6bb024c_0.conda      347.4 MB
urllib3-1.25.11-py_0.conda                    99 KB
certifi-2020.12.5-py37h89c1867_1.tar.bz2     143 KB
tornado-6.1-py37h4abf009_0.tar.bz2           645 KB
keras-2.3.1-py37_0.tar.bz2                   591 KB
keras-preprocessing-1.1.2-pyhd8ed1ab_0.tar.bz2      34 KB
tensorflow-1.13.1-py37h90a7d86_1.tar.bz2    75.5 MB
libtiff-4.1.0-hc3755c2_3.tar.bz2             568 KB
python_abi-3.7-1_cp37m.tar.bz2                 4 KB
cryptography-3.2.1-py37hc72a4ac_0.tar.bz2     623 KB
blas-2.14-openblas.tar.bz2                    10 KB
keras-applications-1.0.8-py_1.tar.bz2         30 KB
pillow-8.0.1-py37h63a5d19_0.tar.bz2          689 KB
libpng-1.6.37-h21135ba_2.tar.bz2             306 KB
scikit-learn-0.22-py37hcdab131_1.tar.bz2     7.1 MB
libprotobuf-3.13.0.1-h8b12597_0.tar.bz2      2.3 MB
jinja2-2.11.3-pyh44b312d_0.tar.bz2            93 KB
hdf5-1.10.6-nompi_h3c11f04_101.tar.bz2       3.0 MB
libgfortran-ng-7.5.0-h14aa051_18.tar.bz2      22 KB
lz4-c-1.9.2-he1b5a44_3.tar.bz2               203 KB
conda-package-handling-1.7.2-py37hb5d75c8_0.tar.bz2     915 KB
pytorch-1.3.1-py3.7_cuda10.1.243_cudnn7.6.3_0.tar.bz2   428.0 MB
python-dateutil-2.8.1-py_0.tar.bz2           220 KB
jpeg-9d-h36c2ea0_0.tar.bz2                   264 KB
zipp-3.4.1-pyhd8ed1ab_0.tar.bz2               11 KB
numpy-base-1.17.4-py37h2f8d375_0.conda       4.1 MB

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/opt/conda/pkgs
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blas-2.14-openblas                            39 KB
numpy-1.17.4-py37hd5be1e1_0                   11 KB
liblapack-3.8.0-14_openblas                   36 KB
liblapacke-3.8.0-14_openblas                  36 KB
libblas-3.8.0-14_openblas                     36 KB
toolchain_c_linux-64-2.4.0-0                  41 KB
libgfortran-ng-7.5.0-h14aa051_18              92 KB
libcblas-3.8.0-14_openblas                    36 KB
python_abi-3.7-1_cp37m                        10 KB
toolchain_cxx_linux-64-2.4.0-0                41 KB

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 ---> 7d452c7ae572
Step 7/9 : RUN pip install allennlp==0.9.0
 ---> Running in 123e5ff2d886
Collecting allennlp==0.9.0
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Requirement already satisfied: joblib in /opt/conda/lib/python3.7/site-packages (from nltk->allennlp==0.9.0) (1.0.1)
Collecting py>=1.8.2
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Collecting attrs>=19.2.0
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Building wheels for collected packages: parsimonious, word2number, ftfy, nltk, overrides
  Building wheel for parsimonious (setup.py): started
  Building wheel for parsimonious (setup.py): finished with status 'done'
  Created wheel for parsimonious: filename=parsimonious-0.8.1-py3-none-any.whl size=42710 sha256=159df02bcd30735ae80e0a982c95494d8ac70fe665c3091a3c0ff0599a62fd03
  Stored in directory: /root/.cache/pip/wheels/88/5d/ba/f27d8af07306b65ee44f9d3f9cadea1db749a421a6db8a99bf
  Building wheel for word2number (setup.py): started
  Building wheel for word2number (setup.py): finished with status 'done'
  Created wheel for word2number: filename=word2number-1.1-py3-none-any.whl size=5586 sha256=562c83e701aa1badd2d9401557370e48aed14aef8dc57a2087b87f4d0a5af532
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  Created wheel for ftfy: filename=ftfy-5.9-py3-none-any.whl size=46451 sha256=66e077a63f9ec0b06753e9bae33af6e5cd533efa7beb5672b659e4660c7cbdbb
  Stored in directory: /root/.cache/pip/wheels/4f/6b/a5/84880e9435707659c6b96d3aadeb9a87a41f61ec9ede469f41
  Building wheel for nltk (setup.py): started
  Building wheel for nltk (setup.py): finished with status 'done'
  Created wheel for nltk: filename=nltk-3.5-py3-none-any.whl size=1434673 sha256=d66accab5afc7ec0158c72659fe0e84cfc76fbdae3b912995b6876d5a2cc3187
  Stored in directory: /root/.cache/pip/wheels/45/6c/46/a1865e7ba706b3817f5d1b2ff7ce8996aabdd0d03d47ba0266
  Building wheel for overrides (setup.py): started
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  Created wheel for overrides: filename=overrides-3.1.0-py3-none-any.whl size=10173 sha256=b5bd9591e0dcc6427511a03ad2e8c570ebe1727ff1d04bb3af11a4536ffe39e2
  Stored in directory: /root/.cache/pip/wheels/3a/0d/38/01a9bc6e20dcfaf0a6a7b552d03137558ba1c38aea47644682
Successfully built parsimonious word2number ftfy nltk overrides
Installing collected packages: jmespath, pytz, cymem, botocore, wasabi, srsly, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, s3transfer, Pygments, preshed, plac, murmurhash, itsdangerous, imagesize, docutils, click, blis, babel, alabaster, zope.interface, zope.event, wcwidth, toml, thinc, sphinx, sentencepiece, regex, py, pluggy, kiwisolver, iniconfig, greenlet, flask, cycler, boto3, attrs, word2number, unidecode, tensorboardX, sqlparse, spacy, responses, pytorch-transformers, pytorch-pretrained-bert, pytest, parsimonious, overrides, numpydoc, nltk, matplotlib, jsonpickle, gevent, ftfy, flask-cors, flaky, editdistance, conllu, allennlp
Killed
The command '/bin/sh -c pip install allennlp==0.9.0' returned a non-zero code: 137
flomock commented 3 years ago

docker build does not require pip install allennlp==0.9.0 anymore. please find the newest version of epidope at: https://github.com/flomock/EpiDope