Console Output

Skipping 6,374 KB.. Full Log
< 
* Curl_http_done: called premature == 0

  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
* Connection #0 to host www.apache.org left intact
* Issue another request to this URL: 'https://archive.apache.org/dist/spark/spark-3.0.1/spark-3.0.1-bin-hadoop3.2.tgz'
*   Trying 138.201.131.134...
* TCP_NODELAY set
* Connected to archive.apache.org (138.201.131.134) port 443 (#1)
* ALPN, offering h2
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
*   CAfile: /etc/ssl/certs/ca-certificates.crt
  CApath: /etc/ssl/certs
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [108 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [4639 bytes data]
* TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [333 bytes data]
* TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
* TLSv1.2 (OUT), TLS change cipher, Client hello (1):
} [1 bytes data]
* TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
* TLSv1.2 (IN), TLS change cipher, Client hello (1):
{ [1 bytes data]
* TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server accepted to use http/1.1
* Server certificate:
*  subject: OU=Domain Control Validated; OU=PositiveSSL Wildcard; CN=*.apache.org
*  start date: Jul  1 00:00:00 2019 GMT
*  expire date: Jun 30 23:59:59 2021 GMT
*  subjectAltName: host "archive.apache.org" matched cert's "*.apache.org"
*  issuer: C=GB; ST=Greater Manchester; L=Salford; O=Sectigo Limited; CN=Sectigo RSA Domain Validation Secure Server CA
*  SSL certificate verify ok.
} [5 bytes data]
> GET /dist/spark/spark-3.0.1/spark-3.0.1-bin-hadoop3.2.tgz HTTP/1.1
> Host: archive.apache.org
> User-Agent: curl/7.52.1
> Accept: */*
> 
{ [5 bytes data]
< HTTP/1.1 200 OK
< Date: Thu, 06 May 2021 18:08:50 GMT
< Server: Apache
< Last-Modified: Fri, 28 Aug 2020 09:25:52 GMT
< ETag: "d5aec3d-5adeca3a117c0"
< Accept-Ranges: bytes
< Content-Length: 224062525
< Content-Type: application/x-gzip
< 

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* Connection #1 to host archive.apache.org left intact

tar xzf ${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}.tgz --directory ${MANGO_TMP_DIR}
+ tar xzf /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2.tgz --directory /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded
export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}
+ export SPARK_HOME=/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2
+ SPARK_HOME=/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2



# create a conda environment for python build, if necessary
pythons=( 3.6 )
+ pythons=(3.6)
for python in ${pythons[*]}
do
    conda create -y -q -c conda-forge -n mango-build-${PYTHON_UUID} python=${python} pip=19.3.1 jupyterlab=2.0.1
    source activate mango-build-${PYTHON_UUID}

    # install npm and node in the venv for mango-pileup
    conda install -y nodejs

    # prepare mango python
    pushd mango-python
    make prepare
    popd

    # we can run the python build, now that we have a spark executable
    # requires SPARK_HOME to be set
    mvn -U \
        -P python,distribution \
        package \
        -DskipTests \
        -Dhadoop.version=${HADOOP_VERSION} \
        -Dspark.version=${SPARK_VERSION}

    # clean mango python
    pushd mango-python
    make clean
    popd

    # prepare mango viz
    pushd mango-pileup
    make prepare
    popd

    # run the widgets tests (mango-pileup)
    mvn -P widgets test

    # clean mango viz
    pushd mango-pileup
    make clean
    popd

    # make sure that the distribution package contains an egg
    # if no assembly jar is found, this will exit with code 1 and fail the build
    tar tzf mango-distribution/target/mango-distribution*-bin.tar.gz | \
        grep bdgenomics.mango | \
        grep egg

    # test mango notebook, output to temporary log file
    MANGO_NOTEBOOK_LOGS=${MANGO_TMP_DIR}/mango-notebook.log

    # notebook args --ip=0.0.0.0 --no-browser --allow-root required for docker
    bash -xv ${PROJECT_ROOT}/bin/mango-notebook -- --ip=0.0.0.0 --no-browser --allow-root &> ${MANGO_NOTEBOOK_LOGS} &

    # sleep for 2 seconds to let mango-notebook start up
    sleep 2

    # if mango-notebook fails, then trying to kill the process will fail
    if kill $! ; then
        echo "Mango Notebook Succeeded"
    else
        echo "Mango Notebook failed with logs:"
        cat ${MANGO_NOTEBOOK_LOGS}
        exit 1
    fi

    # deactivate and remove the conda env
    set +e +x
    source deactivate
    conda remove -y --name mango-build-${PYTHON_UUID} --all
    set -e -x
done
+ for python in ${pythons[*]}
+ conda create -y -q -c conda-forge -n mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290 python=3.6 pip=19.3.1 jupyterlab=2.0.1
Collecting package metadata (current_repodata.json): ...working... done
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: /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290

  added / updated specs:
    - jupyterlab=2.0.1
    - pip=19.3.1
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            1_gnu          22 KB  conda-forge
    argon2-cffi-20.1.0         |   py36h8f6f2f9_2          47 KB  conda-forge
    async_generator-1.10       |             py_0          18 KB  conda-forge
    attrs-20.3.0               |     pyhd3deb0d_0          41 KB  conda-forge
    backcall-0.2.0             |     pyh9f0ad1d_0          13 KB  conda-forge
    backports-1.0              |             py_2           4 KB  conda-forge
    backports.functools_lru_cache-1.6.4|     pyhd8ed1ab_0           9 KB  conda-forge
    bleach-3.3.0               |     pyh44b312d_0         111 KB  conda-forge
    brotlipy-0.7.0             |py36h8f6f2f9_1001         341 KB  conda-forge
    ca-certificates-2020.12.5  |       ha878542_0         137 KB  conda-forge
    certifi-2020.12.5          |   py36h5fab9bb_1         143 KB  conda-forge
    cffi-1.14.5                |   py36hc120d54_0         225 KB  conda-forge
    chardet-4.0.0              |   py36h5fab9bb_1         219 KB  conda-forge
    cryptography-3.4.7         |   py36hb60f036_0         1.1 MB  conda-forge
    decorator-5.0.7            |     pyhd8ed1ab_0          11 KB  conda-forge
    defusedxml-0.7.1           |     pyhd8ed1ab_0          23 KB  conda-forge
    entrypoints-0.3            |  pyhd8ed1ab_1003           8 KB  conda-forge
    idna-2.10                  |     pyh9f0ad1d_0          52 KB  conda-forge
    importlib-metadata-4.0.1   |   py36h5fab9bb_0          30 KB  conda-forge
    ipykernel-5.5.4            |   py36hcb3619a_0         166 KB  conda-forge
    ipython-7.16.1             |   py36he448a4c_2         1.1 MB  conda-forge
    ipython_genutils-0.2.0     |             py_1          21 KB  conda-forge
    jedi-0.17.2                |   py36h5fab9bb_1         957 KB  conda-forge
    jinja2-2.11.3              |     pyh44b312d_0          93 KB  conda-forge
    json5-0.9.5                |     pyh9f0ad1d_0          20 KB  conda-forge
    jsonschema-3.2.0           |     pyhd8ed1ab_3          45 KB  conda-forge
    jupyter_client-6.1.12      |     pyhd8ed1ab_0          79 KB  conda-forge
    jupyter_core-4.7.1         |   py36h5fab9bb_0          72 KB  conda-forge
    jupyterlab-2.0.1           |             py_0         5.7 MB  conda-forge
    jupyterlab_pygments-0.1.2  |     pyh9f0ad1d_0           8 KB  conda-forge
    jupyterlab_server-1.2.0    |             py_0          25 KB  conda-forge
    ld_impl_linux-64-2.35.1    |       hea4e1c9_2         618 KB  conda-forge
    libffi-3.3                 |       h58526e2_2          51 KB  conda-forge
    libgcc-ng-9.3.0            |      h2828fa1_19         7.8 MB  conda-forge
    libgomp-9.3.0              |      h2828fa1_19         376 KB  conda-forge
    libsodium-1.0.18           |       h36c2ea0_1         366 KB  conda-forge
    libstdcxx-ng-9.3.0         |      h6de172a_19         4.0 MB  conda-forge
    markupsafe-1.1.1           |   py36h8f6f2f9_3          27 KB  conda-forge
    mistune-0.8.4              |py36h8f6f2f9_1003          54 KB  conda-forge
    nbclient-0.5.3             |     pyhd8ed1ab_0          67 KB  conda-forge
    nbconvert-6.0.7            |   py36h5fab9bb_3         533 KB  conda-forge
    nbformat-5.1.3             |     pyhd8ed1ab_0          47 KB  conda-forge
    ncurses-6.2                |       h58526e2_4         985 KB  conda-forge
    nest-asyncio-1.5.1         |     pyhd8ed1ab_0           9 KB  conda-forge
    notebook-6.3.0             |   py36h5fab9bb_0         6.3 MB  conda-forge
    openssl-1.1.1k             |       h7f98852_0         2.1 MB  conda-forge
    packaging-20.9             |     pyh44b312d_0          35 KB  conda-forge
    pandoc-2.12                |       h7f98852_0        12.4 MB  conda-forge
    pandocfilters-1.4.2        |             py_1           9 KB  conda-forge
    parso-0.7.1                |     pyh9f0ad1d_0          70 KB  conda-forge
    pexpect-4.8.0              |     pyh9f0ad1d_2          47 KB  conda-forge
    pickleshare-0.7.5          |          py_1003           9 KB  conda-forge
    pip-19.3.1                 |           py36_0         1.9 MB  conda-forge
    prometheus_client-0.10.1   |     pyhd8ed1ab_0          46 KB  conda-forge
    prompt-toolkit-3.0.18      |     pyha770c72_0         244 KB  conda-forge
    ptyprocess-0.7.0           |     pyhd3deb0d_0          16 KB  conda-forge
    pycparser-2.20             |     pyh9f0ad1d_2          94 KB  conda-forge
    pygments-2.9.0             |     pyhd8ed1ab_0         754 KB  conda-forge
    pyopenssl-20.0.1           |     pyhd8ed1ab_0          48 KB  conda-forge
    pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  conda-forge
    pyrsistent-0.17.3          |   py36h8f6f2f9_2          89 KB  conda-forge
    pysocks-1.7.1              |   py36h5fab9bb_3          27 KB  conda-forge
    python-3.6.13              |hffdb5ce_0_cpython        38.4 MB  conda-forge
    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge
    python_abi-3.6             |          1_cp36m           4 KB  conda-forge
    pyzmq-22.0.3               |   py36h7068817_1         496 KB  conda-forge
    readline-8.1               |       h46c0cb4_0         295 KB  conda-forge
    requests-2.25.1            |     pyhd3deb0d_0          51 KB  conda-forge
    send2trash-1.5.0           |             py_0          12 KB  conda-forge
    setuptools-49.6.0          |   py36h5fab9bb_3         936 KB  conda-forge
    six-1.16.0                 |     pyh6c4a22f_0          14 KB  conda-forge
    sqlite-3.35.5              |       h74cdb3f_0         1.4 MB  conda-forge
    terminado-0.9.4            |   py36h5fab9bb_0          26 KB  conda-forge
    testpath-0.4.4             |             py_0          85 KB  conda-forge
    tk-8.6.10                  |       h21135ba_1         3.2 MB  conda-forge
    tornado-6.1                |   py36h8f6f2f9_1         643 KB  conda-forge
    traitlets-4.3.3            |   py36h9f0ad1d_1         133 KB  conda-forge
    typing_extensions-3.7.4.3  |             py_0          25 KB  conda-forge
    urllib3-1.26.4             |     pyhd8ed1ab_0          99 KB  conda-forge
    wcwidth-0.2.5              |     pyh9f0ad1d_2          33 KB  conda-forge
    webencodings-0.5.1         |             py_1          12 KB  conda-forge
    wheel-0.36.2               |     pyhd3deb0d_0          31 KB  conda-forge
    xz-5.2.5                   |       h516909a_1         343 KB  conda-forge
    zeromq-4.3.4               |       h9c3ff4c_0         352 KB  conda-forge
    zipp-3.4.1                 |     pyhd8ed1ab_0          11 KB  conda-forge
    zlib-1.2.11                |    h516909a_1010         106 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        96.7 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  argon2-cffi        conda-forge/linux-64::argon2-cffi-20.1.0-py36h8f6f2f9_2
  async_generator    conda-forge/noarch::async_generator-1.10-py_0
  attrs              conda-forge/noarch::attrs-20.3.0-pyhd3deb0d_0
  backcall           conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
  backports          conda-forge/noarch::backports-1.0-py_2
  backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0
  bleach             conda-forge/noarch::bleach-3.3.0-pyh44b312d_0
  brotlipy           conda-forge/linux-64::brotlipy-0.7.0-py36h8f6f2f9_1001
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
  certifi            conda-forge/linux-64::certifi-2020.12.5-py36h5fab9bb_1
  cffi               conda-forge/linux-64::cffi-1.14.5-py36hc120d54_0
  chardet            conda-forge/linux-64::chardet-4.0.0-py36h5fab9bb_1
  cryptography       conda-forge/linux-64::cryptography-3.4.7-py36hb60f036_0
  decorator          conda-forge/noarch::decorator-5.0.7-pyhd8ed1ab_0
  defusedxml         conda-forge/noarch::defusedxml-0.7.1-pyhd8ed1ab_0
  entrypoints        conda-forge/noarch::entrypoints-0.3-pyhd8ed1ab_1003
  idna               conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
  importlib-metadata conda-forge/linux-64::importlib-metadata-4.0.1-py36h5fab9bb_0
  ipykernel          conda-forge/linux-64::ipykernel-5.5.4-py36hcb3619a_0
  ipython            conda-forge/linux-64::ipython-7.16.1-py36he448a4c_2
  ipython_genutils   conda-forge/noarch::ipython_genutils-0.2.0-py_1
  jedi               conda-forge/linux-64::jedi-0.17.2-py36h5fab9bb_1
  jinja2             conda-forge/noarch::jinja2-2.11.3-pyh44b312d_0
  json5              conda-forge/noarch::json5-0.9.5-pyh9f0ad1d_0
  jsonschema         conda-forge/noarch::jsonschema-3.2.0-pyhd8ed1ab_3
  jupyter_client     conda-forge/noarch::jupyter_client-6.1.12-pyhd8ed1ab_0
  jupyter_core       conda-forge/linux-64::jupyter_core-4.7.1-py36h5fab9bb_0
  jupyterlab         conda-forge/noarch::jupyterlab-2.0.1-py_0
  jupyterlab_pygmen~ conda-forge/noarch::jupyterlab_pygments-0.1.2-pyh9f0ad1d_0
  jupyterlab_server  conda-forge/noarch::jupyterlab_server-1.2.0-py_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_2
  libffi             conda-forge/linux-64::libffi-3.3-h58526e2_2
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_19
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h2828fa1_19
  libsodium          conda-forge/linux-64::libsodium-1.0.18-h36c2ea0_1
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_19
  markupsafe         conda-forge/linux-64::markupsafe-1.1.1-py36h8f6f2f9_3
  mistune            conda-forge/linux-64::mistune-0.8.4-py36h8f6f2f9_1003
  nbclient           conda-forge/noarch::nbclient-0.5.3-pyhd8ed1ab_0
  nbconvert          conda-forge/linux-64::nbconvert-6.0.7-py36h5fab9bb_3
  nbformat           conda-forge/noarch::nbformat-5.1.3-pyhd8ed1ab_0
  ncurses            conda-forge/linux-64::ncurses-6.2-h58526e2_4
  nest-asyncio       conda-forge/noarch::nest-asyncio-1.5.1-pyhd8ed1ab_0
  notebook           conda-forge/linux-64::notebook-6.3.0-py36h5fab9bb_0
  openssl            conda-forge/linux-64::openssl-1.1.1k-h7f98852_0
  packaging          conda-forge/noarch::packaging-20.9-pyh44b312d_0
  pandoc             conda-forge/linux-64::pandoc-2.12-h7f98852_0
  pandocfilters      conda-forge/noarch::pandocfilters-1.4.2-py_1
  parso              conda-forge/noarch::parso-0.7.1-pyh9f0ad1d_0
  pexpect            conda-forge/noarch::pexpect-4.8.0-pyh9f0ad1d_2
  pickleshare        conda-forge/noarch::pickleshare-0.7.5-py_1003
  pip                conda-forge/linux-64::pip-19.3.1-py36_0
  prometheus_client  conda-forge/noarch::prometheus_client-0.10.1-pyhd8ed1ab_0
  prompt-toolkit     conda-forge/noarch::prompt-toolkit-3.0.18-pyha770c72_0
  ptyprocess         conda-forge/noarch::ptyprocess-0.7.0-pyhd3deb0d_0
  pycparser          conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2
  pygments           conda-forge/noarch::pygments-2.9.0-pyhd8ed1ab_0
  pyopenssl          conda-forge/noarch::pyopenssl-20.0.1-pyhd8ed1ab_0
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  pyrsistent         conda-forge/linux-64::pyrsistent-0.17.3-py36h8f6f2f9_2
  pysocks            conda-forge/linux-64::pysocks-1.7.1-py36h5fab9bb_3
  python             conda-forge/linux-64::python-3.6.13-hffdb5ce_0_cpython
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/linux-64::python_abi-3.6-1_cp36m
  pyzmq              conda-forge/linux-64::pyzmq-22.0.3-py36h7068817_1
  readline           conda-forge/linux-64::readline-8.1-h46c0cb4_0
  requests           conda-forge/noarch::requests-2.25.1-pyhd3deb0d_0
  send2trash         conda-forge/noarch::send2trash-1.5.0-py_0
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py36h5fab9bb_3
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  sqlite             conda-forge/linux-64::sqlite-3.35.5-h74cdb3f_0
  terminado          conda-forge/linux-64::terminado-0.9.4-py36h5fab9bb_0
  testpath           conda-forge/noarch::testpath-0.4.4-py_0
  tk                 conda-forge/linux-64::tk-8.6.10-h21135ba_1
  tornado            conda-forge/linux-64::tornado-6.1-py36h8f6f2f9_1
  traitlets          conda-forge/linux-64::traitlets-4.3.3-py36h9f0ad1d_1
  typing_extensions  conda-forge/noarch::typing_extensions-3.7.4.3-py_0
  urllib3            conda-forge/noarch::urllib3-1.26.4-pyhd8ed1ab_0
  wcwidth            conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_2
  webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zeromq             conda-forge/linux-64::zeromq-4.3.4-h9c3ff4c_0
  zipp               conda-forge/noarch::zipp-3.4.1-pyhd8ed1ab_0
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1010


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ source activate mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290
#!/bin/sh
_CONDA_ROOT="/opt/conda"
++ _CONDA_ROOT=/opt/conda
# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
\. "$_CONDA_ROOT/etc/profile.d/conda.sh" || return $?
++ . /opt/conda/etc/profile.d/conda.sh
export CONDA_EXE='/opt/conda/bin/conda'
+++ export CONDA_EXE=/opt/conda/bin/conda
+++ CONDA_EXE=/opt/conda/bin/conda
export _CE_M=''
+++ export _CE_M=
+++ _CE_M=
export _CE_CONDA=''
+++ export _CE_CONDA=
+++ _CE_CONDA=
export CONDA_PYTHON_EXE='/opt/conda/bin/python'
+++ export CONDA_PYTHON_EXE=/opt/conda/bin/python
+++ CONDA_PYTHON_EXE=/opt/conda/bin/python

# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause

__add_sys_prefix_to_path() {
    # In dev-mode CONDA_EXE is python.exe and on Windows
    # it is in a different relative location to condabin.
    if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then
        SYSP=$(\dirname "${CONDA_EXE}")
    else
        SYSP=$(\dirname "${CONDA_EXE}")
        SYSP=$(\dirname "${SYSP}")
    fi

    if [ -n "${WINDIR+x}" ]; then
        PATH="${SYSP}/bin:${PATH}"
        PATH="${SYSP}/Scripts:${PATH}"
        PATH="${SYSP}/Library/bin:${PATH}"
        PATH="${SYSP}/Library/usr/bin:${PATH}"
        PATH="${SYSP}/Library/mingw-w64/bin:${PATH}"
        PATH="${SYSP}:${PATH}"
    else
        PATH="${SYSP}/bin:${PATH}"
    fi
    \export PATH
}

__conda_hashr() {
    if [ -n "${ZSH_VERSION:+x}" ]; then
        \rehash
    elif [ -n "${POSH_VERSION:+x}" ]; then
        :  # pass
    else
        \hash -r
    fi
}

__conda_activate() {
    if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
        # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
        # after conda updated to >= 4.4. See issue #6173.
        PS1="$CONDA_PS1_BACKUP"
        \unset CONDA_PS1_BACKUP
    fi

    \local cmd="$1"
    shift
    \local ask_conda
    CONDA_INTERNAL_OLDPATH="${PATH}"
    __add_sys_prefix_to_path
    ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix "$cmd" "$@")" || \return $?
    rc=$?
    PATH="${CONDA_INTERNAL_OLDPATH}"
    \eval "$ask_conda"
    if [ $rc != 0 ]; then
        \export PATH
    fi
    __conda_hashr
}

__conda_reactivate() {
    \local ask_conda
    CONDA_INTERNAL_OLDPATH="${PATH}"
    __add_sys_prefix_to_path
    ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix reactivate)" || \return $?
    PATH="${CONDA_INTERNAL_OLDPATH}"
    \eval "$ask_conda"
    __conda_hashr
}

conda() {
    if [ "$#" -lt 1 ]; then
        "$CONDA_EXE" $_CE_M $_CE_CONDA
    else
        \local cmd="$1"
        shift
        case "$cmd" in
            activate|deactivate)
                __conda_activate "$cmd" "$@"
                ;;
            install|update|upgrade|remove|uninstall)
                CONDA_INTERNAL_OLDPATH="${PATH}"
                __add_sys_prefix_to_path
                "$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
                \local t1=$?
                PATH="${CONDA_INTERNAL_OLDPATH}"
                if [ $t1 = 0 ]; then
                    __conda_reactivate
                else
                    return $t1
                fi
                ;;
            *)
                CONDA_INTERNAL_OLDPATH="${PATH}"
                __add_sys_prefix_to_path
                "$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
                \local t1=$?
                PATH="${CONDA_INTERNAL_OLDPATH}"
                return $t1
                ;;
        esac
    fi
}

if [ -z "${CONDA_SHLVL+x}" ]; then
    \export CONDA_SHLVL=0
    # In dev-mode CONDA_EXE is python.exe and on Windows
    # it is in a different relative location to condabin.
    if [ -n "${_CE_CONDA+x}" ] && [ -n "${WINDIR+x}" ]; then
        PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
    else
        PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
    fi
    \export PATH

    # We're not allowing PS1 to be unbound. It must at least be set.
    # However, we're not exporting it, which can cause problems when starting a second shell
    # via a first shell (i.e. starting zsh from bash).
    if [ -z "${PS1+x}" ]; then
        PS1=
    fi
fi
+++ '[' -z '' ']'
+++ export CONDA_SHLVL=0
+++ CONDA_SHLVL=0
+++ '[' -n x ']'
+++ '[' -n '' ']'
+++++ dirname /opt/conda/bin/conda
++++ dirname /opt/conda/bin
+++ PATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ export PATH
+++ '[' -z '' ']'
+++ PS1=
conda activate "$@"
++ conda activate mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290
++ '[' 2 -lt 1 ']'
++ local cmd=activate
++ shift
++ case "$cmd" in
++ __conda_activate activate mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290
++ '[' -n '' ']'
++ local cmd=activate
++ shift
++ local ask_conda
++ CONDA_INTERNAL_OLDPATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ __add_sys_prefix_to_path
++ '[' -n '' ']'
+++ dirname /opt/conda/bin/conda
++ SYSP=/opt/conda/bin
+++ dirname /opt/conda/bin
++ SYSP=/opt/conda
++ '[' -n '' ']'
++ PATH=/opt/conda/bin:/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export PATH
+++ PS1=
+++ /opt/conda/bin/conda shell.posix activate mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290
++ ask_conda='PS1='\''(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '\''
export PATH='\''/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290'\''
export CONDA_PROMPT_MODIFIER='\''(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '\''
export CONDA_EXE='\''/opt/conda/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/conda/bin/python'\'''
++ rc=0
++ PATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ eval 'PS1='\''(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '\''
export PATH='\''/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290'\''
export CONDA_PROMPT_MODIFIER='\''(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '\''
export CONDA_EXE='\''/opt/conda/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/conda/bin/python'\'''
PS1='(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
+++ PS1='(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
export PATH='/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
+++ export PATH=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ PATH=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
export CONDA_PREFIX='/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290'
+++ export CONDA_PREFIX=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290
+++ CONDA_PREFIX=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290
export CONDA_SHLVL='1'
+++ export CONDA_SHLVL=1
+++ CONDA_SHLVL=1
export CONDA_DEFAULT_ENV='mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290'
+++ export CONDA_DEFAULT_ENV=mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290
+++ CONDA_DEFAULT_ENV=mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290
export CONDA_PROMPT_MODIFIER='(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
+++ export 'CONDA_PROMPT_MODIFIER=(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
+++ CONDA_PROMPT_MODIFIER='(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
export CONDA_EXE='/opt/conda/bin/conda'
+++ export CONDA_EXE=/opt/conda/bin/conda
+++ CONDA_EXE=/opt/conda/bin/conda
export _CE_M=''
+++ export _CE_M=
+++ _CE_M=
export _CE_CONDA=''
+++ export _CE_CONDA=
+++ _CE_CONDA=
export CONDA_PYTHON_EXE='/opt/conda/bin/python'
+++ export CONDA_PYTHON_EXE=/opt/conda/bin/python
+++ CONDA_PYTHON_EXE=/opt/conda/bin/python
++ '[' 0 '!=' 0 ']'
++ __conda_hashr
++ '[' -n '' ']'
++ '[' -n '' ']'
++ hash -r
+ conda install -y nodejs
+ '[' 3 -lt 1 ']'
+ local cmd=install
+ shift
+ case "$cmd" in
+ CONDA_INTERNAL_OLDPATH=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/conda/bin/conda
+ SYSP=/opt/conda/bin
++ dirname /opt/conda/bin
+ SYSP=/opt/conda
+ '[' -n '' ']'
+ PATH=/opt/conda/bin:/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
+ /opt/conda/bin/conda install -y nodejs
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290

  added / updated specs:
    - nodejs


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2021.4.13  |       h06a4308_1         114 KB
    certifi-2020.12.5          |   py36h06a4308_0         140 KB
    icu-68.1                   |       h2531618_0        11.8 MB
    libuv-1.40.0               |       h7b6447c_0         736 KB
    nodejs-14.8.0              |       hda19d22_0        13.2 MB
    openssl-1.1.1k             |       h27cfd23_0         2.5 MB
    ------------------------------------------------------------
                                           Total:        28.5 MB

The following NEW packages will be INSTALLED:

  icu                pkgs/main/linux-64::icu-68.1-h2531618_0
  libuv              pkgs/main/linux-64::libuv-1.40.0-h7b6447c_0
  nodejs             pkgs/main/linux-64::nodejs-14.8.0-hda19d22_0

The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.12.~ --> pkgs/main::ca-certificates-2021.4.13-h06a4308_1

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

  certifi            conda-forge::certifi-2020.12.5-py36h5~ --> pkgs/main::certifi-2020.12.5-py36h06a4308_0
  openssl            conda-forge::openssl-1.1.1k-h7f98852_0 --> pkgs/main::openssl-1.1.1k-h27cfd23_0



Downloading and Extracting Packages

certifi-2020.12.5    | 140 KB    |            |   0% 
certifi-2020.12.5    | 140 KB    | ########## | 100% 

icu-68.1             | 11.8 MB   |            |   0% 
icu-68.1             | 11.8 MB   | ####       |  40% 
icu-68.1             | 11.8 MB   | ########## | 100% 
icu-68.1             | 11.8 MB   | ########## | 100% 

ca-certificates-2021 | 114 KB    |            |   0% 
ca-certificates-2021 | 114 KB    | ########## | 100% 

libuv-1.40.0         | 736 KB    |            |   0% 
libuv-1.40.0         | 736 KB    | ########## | 100% 

openssl-1.1.1k       | 2.5 MB    |            |   0% 
openssl-1.1.1k       | 2.5 MB    | ########## | 100% 
openssl-1.1.1k       | 2.5 MB    | ########## | 100% 

nodejs-14.8.0        | 13.2 MB   |            |   0% 
nodejs-14.8.0        | 13.2 MB   | ####6      |  46% 
nodejs-14.8.0        | 13.2 MB   | ########## | 100% 
nodejs-14.8.0        | 13.2 MB   | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.4
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


+ local t1=0
+ PATH=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ '[' 0 = 0 ']'
+ __conda_reactivate
+ local ask_conda
+ CONDA_INTERNAL_OLDPATH=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/conda/bin/conda
+ SYSP=/opt/conda/bin
++ dirname /opt/conda/bin
+ SYSP=/opt/conda
+ '[' -n '' ']'
+ PATH=/opt/conda/bin:/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
++ PS1='(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
++ /opt/conda/bin/conda shell.posix reactivate
+ ask_conda='PS1='\''(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '\''
export PATH='\''/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '\'''
+ PATH=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ eval 'PS1='\''(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '\''
export PATH='\''/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '\'''
PS1='(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
++ PS1='(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
export PATH='/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
++ export PATH=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ PATH=/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
export CONDA_SHLVL='1'
++ export CONDA_SHLVL=1
++ CONDA_SHLVL=1
export CONDA_PROMPT_MODIFIER='(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
++ export 'CONDA_PROMPT_MODIFIER=(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
++ CONDA_PROMPT_MODIFIER='(mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290) '
+ __conda_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ pushd mango-python
+ make prepare
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded /home
which pip
/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin/pip
# ipython version required for python 2.7
pip install -r requirements.txt
Collecting cigar==0.1.3
  Downloading https://files.pythonhosted.org/packages/2d/5f/ffa58a8c64f811772b69a01eeab25c602b72d02a0c83006177c21abedaa3/cigar-0.1.3.tar.gz
Collecting matplotlib==2.0.2
  Downloading https://files.pythonhosted.org/packages/60/d4/6b6d8a7a6bc69a1602ab372f6fc6e88ef88a8a96398a1a25edbac636295b/matplotlib-2.0.2-cp36-cp36m-manylinux1_x86_64.whl (14.6MB)
Collecting ipython==7.8.0
  Downloading https://files.pythonhosted.org/packages/fb/44/f28a13852e562af719f9de1761680a84a93e8b4c50e22d00d68f60ee2e8b/ipython-7.8.0-py3-none-any.whl (775kB)
Collecting jupyter==1.0.0
  Downloading https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl
Collecting bdgenomics.adam==0.34.0
  Downloading https://files.pythonhosted.org/packages/43/11/6e7ad2b43675ed182e142fc67de509d36d86d23b1fbe44e4af1c873985a1/bdgenomics.adam-0.34.0.tar.gz (41.1MB)
Collecting bdgenomics.mango.pileup==0.0.6a0
  Downloading https://files.pythonhosted.org/packages/48/8f/06f3e694caf8ba67dadbfca5c7f050343e7e3363ba348d94a224aa964cfb/bdgenomics.mango.pileup-0.0.6a0.tar.gz (892kB)
Collecting ipywidgets==7.0.0
  Downloading https://files.pythonhosted.org/packages/14/ea/793f6588d5be295d103fb868e26ba8671686b70bd855a21d02302f8dcd37/ipywidgets-7.0.0-py2.py3-none-any.whl (64kB)
Collecting psutil
  Downloading https://files.pythonhosted.org/packages/da/82/56cd16a4c5f53e3e5dd7b2c30d5c803e124f218ebb644ca9c30bc907eadd/psutil-5.8.0-cp36-cp36m-manylinux2010_x86_64.whl (291kB)
Collecting pytest==3.9.1
  Downloading https://files.pythonhosted.org/packages/bf/14/a16e1ac03aeb9776d98374bb76495a6623d56dff0f7b815ed5a1e04d893e/pytest-3.9.1-py2.py3-none-any.whl (213kB)
Collecting jupyter_contrib_nbextensions
  Downloading https://files.pythonhosted.org/packages/33/f0/6e2c00afda860f655fbf0f795f7310bdbf12122846344dfdc803fc7455d5/jupyter_contrib_nbextensions-0.5.1-py2.py3-none-any.whl (20.9MB)
Requirement already satisfied: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.4.7)
Collecting pytz
  Downloading https://files.pythonhosted.org/packages/70/94/784178ca5dd892a98f113cdd923372024dc04b8d40abe77ca76b5fb90ca6/pytz-2021.1-py2.py3-none-any.whl (510kB)
Collecting numpy>=1.7.1
  Downloading https://files.pythonhosted.org/packages/14/32/d3fa649ad7ec0b82737b92fefd3c4dd376b0bb23730715124569f38f3a08/numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl (14.8MB)
Requirement already satisfied: python-dateutil in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.8.1)
Collecting cycler>=0.10
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Requirement already satisfied: six>=1.10 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.16.0)
Requirement already satisfied: pygments in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (2.9.0)
Collecting prompt-toolkit<2.1.0,>=2.0.0
  Downloading https://files.pythonhosted.org/packages/87/61/2dfea88583d5454e3a64f9308a686071d58d59a55db638268a6413e1eb6d/prompt_toolkit-2.0.10-py3-none-any.whl (340kB)
Requirement already satisfied: pickleshare in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.7.5)
Requirement already satisfied: backcall in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.2.0)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.17.2)
Requirement already satisfied: traitlets>=4.2 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (4.3.3)
Requirement already satisfied: decorator in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (5.0.7)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (4.8.0)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (49.6.0.post20210108)
Requirement already satisfied: nbconvert in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (6.0.7)
Collecting jupyter-console
  Downloading https://files.pythonhosted.org/packages/59/cd/aa2670ffc99eb3e5bbe2294c71e4bf46a9804af4f378d09d7a8950996c9b/jupyter_console-6.4.0-py3-none-any.whl
Requirement already satisfied: notebook in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (6.3.0)
Collecting qtconsole
  Downloading https://files.pythonhosted.org/packages/90/72/3f81d75611bcd4634ae1785efd9f5afbed06ce2b810e4dee28061a2c3895/qtconsole-5.1.0-py3-none-any.whl (119kB)
Requirement already satisfied: ipykernel in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.5.4)
Collecting pyspark>=1.6.0
  Downloading https://files.pythonhosted.org/packages/45/b0/9d6860891ab14a39d4bddf80ba26ce51c2f9dc4805e5c6978ac0472c120a/pyspark-3.1.1.tar.gz (212.3MB)
Collecting modin[ray]==0.6.1
  Downloading https://files.pythonhosted.org/packages/4f/62/dbea5f16c685aa1bab65787562f4990d5b78caa915c7d323b47013c454ad/modin-0.6.1-py3-none-any.whl (230kB)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 7)) (5.1.3)
Collecting widgetsnbextension~=3.0.0
  Downloading https://files.pythonhosted.org/packages/8d/f2/c8bcccccbed39d51d3e237fb0c0f0c9bbc845d12afc41f5ca5f5728fffc7/widgetsnbextension-3.0.8-py2.py3-none-any.whl (2.2MB)
Collecting py>=1.5.0
  Downloading https://files.pythonhosted.org/packages/67/32/6fe01cfc3d1a27c92fdbcdfc3f67856da8cbadf0dd9f2e18055202b2dc62/py-1.10.0-py2.py3-none-any.whl (97kB)
Collecting more-itertools>=4.0.0
  Downloading https://files.pythonhosted.org/packages/05/47/514062a0798c2e9bdfd4514bacf9971fc8961b715f01487e4cfda3cc45a7/more_itertools-8.7.0-py3-none-any.whl (48kB)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from pytest==3.9.1->-r requirements.txt (line 9)) (20.3.0)
Collecting atomicwrites>=1.0
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Collecting jupyter-latex-envs>=1.3.8
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Collecting jupyter-contrib-core>=0.3.3
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Collecting lxml
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Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.4.2)
Requirement already satisfied: jupyter-client in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter-console->jupyter==1.0.0->-r requirements.txt (line 4)) (6.1.12)
Requirement already satisfied: Send2Trash>=1.5.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.5.0)
Requirement already satisfied: terminado>=0.8.3 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.9.4)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (22.0.3)
Requirement already satisfied: argon2-cffi in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (20.1.0)
Requirement already satisfied: prometheus-client in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.10.1)
Collecting qtpy
  Downloading https://files.pythonhosted.org/packages/cd/fd/9972948f02e967b691cc0ca1f26124826a3b88cb38f412a8b7935b8c3c72/QtPy-1.9.0-py2.py3-none-any.whl (54kB)
Collecting py4j==0.10.9
  Downloading https://files.pythonhosted.org/packages/9e/b6/6a4fb90cd235dc8e265a6a2067f2a2c99f0d91787f06aca4bcf7c23f3f80/py4j-0.10.9-py2.py3-none-any.whl (198kB)
Collecting pandas==0.25.1
  Downloading https://files.pythonhosted.org/packages/73/9b/52e228545d14f14bb2a1622e225f38463c8726645165e1cb7dde95bfe6d4/pandas-0.25.1-cp36-cp36m-manylinux1_x86_64.whl (10.5MB)
Collecting ray==0.7.3; extra == "ray"
  Downloading https://files.pythonhosted.org/packages/a7/21/de080b8458de41fd8ac20dd96547418c0ed94eab4359e5885f4041d61337/ray-0.7.3-cp36-cp36m-manylinux1_x86_64.whl (48.5MB)
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Requirement already satisfied: webencodings in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5.1)
Requirement already satisfied: packaging in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (20.9)
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Collecting colorama
  Downloading https://files.pythonhosted.org/packages/44/98/5b86278fbbf250d239ae0ecb724f8572af1c91f4a11edf4d36a206189440/colorama-0.4.4-py2.py3-none-any.whl
Collecting filelock
  Downloading https://files.pythonhosted.org/packages/93/83/71a2ee6158bb9f39a90c0dea1637f81d5eef866e188e1971a1b1ab01a35a/filelock-3.0.12-py3-none-any.whl
Collecting funcsigs
  Downloading https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting protobuf>=3.8.0
  Downloading https://files.pythonhosted.org/packages/8c/78/3bccd7f228179b382441644f1692cdce6e0f46b0422e61a39915c98b3287/protobuf-3.15.8-cp36-cp36m-manylinux1_x86_64.whl (1.0MB)
Collecting redis
  Downloading https://files.pythonhosted.org/packages/a7/7c/24fb0511df653cf1a5d938d8f5d19802a88cef255706fdda242ff97e91b7/redis-3.5.3-py2.py3-none-any.whl (72kB)
Collecting click
  Downloading https://files.pythonhosted.org/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82kB)
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Requirement already satisfied: pycparser in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (2.20)
Building wheels for collected packages: cigar, bdgenomics.adam, bdgenomics.mango.pileup, pyspark, jupyter-latex-envs, jupyter-nbextensions-configurator
  Building wheel for cigar (setup.py): started
  Building wheel for cigar (setup.py): finished with status 'done'
  Created wheel for cigar: filename=cigar-0.1.3-cp36-none-any.whl size=4022 sha256=d659f8533e221e72728a9256c0811cba78a6e6ff2f22e342387809a309d6f3bf
  Stored in directory: /home/jenkins/.cache/pip/wheels/eb/c0/e6/f0f525ada263f7f72f4b3efcc7f5b3c12a372f07f55a2d687d
  Building wheel for bdgenomics.adam (setup.py): started
  Building wheel for bdgenomics.adam (setup.py): finished with status 'done'
  Created wheel for bdgenomics.adam: filename=bdgenomics.adam-0.34.0-cp36-none-any.whl size=41105457 sha256=04c1418e2ac863e1116a24841caf8db89720e2ecde6547d0421b1485ea0b264d
  Stored in directory: /home/jenkins/.cache/pip/wheels/63/af/5b/5b9830bf01535c7728c35ce0e3b0b3196ad4219ec0010dd826
  Building wheel for bdgenomics.mango.pileup (setup.py): started
  Building wheel for bdgenomics.mango.pileup (setup.py): finished with status 'done'
  Created wheel for bdgenomics.mango.pileup: filename=bdgenomics.mango.pileup-0.0.6a0-cp36-none-any.whl size=1798435 sha256=dd3bd38a342e64eab591745d69e5bcbc7ced065f97ab1ed761dc6c004f9db22d
  Stored in directory: /home/jenkins/.cache/pip/wheels/ec/df/8e/7e6efc45fd34e2850763a5ec5ac7f27052424d26105f12f971
  Building wheel for pyspark (setup.py): started
  Building wheel for pyspark (setup.py): finished with status 'done'
  Created wheel for pyspark: filename=pyspark-3.1.1-py2.py3-none-any.whl size=212767604 sha256=c649541c7b32f58a102e6528830245212d080c446b13aab932353312deb6001a
  Stored in directory: /home/jenkins/.cache/pip/wheels/0b/90/c0/01de724414ef122bd05f056541fb6a0ecf47c7ca655f8b3c0f
  Building wheel for jupyter-latex-envs (setup.py): started
  Building wheel for jupyter-latex-envs (setup.py): finished with status 'done'
  Created wheel for jupyter-latex-envs: filename=jupyter_latex_envs-1.4.6-py2.py3-none-any.whl size=963394 sha256=5ae56158fee155ce08246d4746d4fd467a914be1f547561654fb34a001e96857
  Stored in directory: /home/jenkins/.cache/pip/wheels/0d/71/2a/164491997299b9f2479a251e254323fe35d946779e18f27956
  Building wheel for jupyter-nbextensions-configurator (setup.py): started
  Building wheel for jupyter-nbextensions-configurator (setup.py): finished with status 'done'
  Created wheel for jupyter-nbextensions-configurator: filename=jupyter_nbextensions_configurator-0.4.1-py2.py3-none-any.whl size=465825 sha256=4c5b0fa6a0d1e037c6f5da45af8ce7e9fe7f030052b44a7c0d7d0ea9f7948c9e
  Stored in directory: /home/jenkins/.cache/pip/wheels/15/df/fe/2a74fe34709e7fdc5ae153a768675d9fda93cc7d5133ed1fb0
Successfully built cigar bdgenomics.adam bdgenomics.mango.pileup pyspark jupyter-latex-envs jupyter-nbextensions-configurator
ERROR: bdgenomics-mango-pileup 0.0.6a0 has requirement pytest==2.8.3, but you'll have pytest 3.9.1 which is incompatible.
ERROR: bdgenomics-mango-pileup 0.0.6a0 has requirement six==1.11.0, but you'll have six 1.16.0 which is incompatible.
Installing collected packages: cigar, pytz, numpy, cycler, matplotlib, prompt-toolkit, ipython, jupyter-console, qtpy, qtconsole, widgetsnbextension, ipywidgets, jupyter, py4j, pyspark, bdgenomics.adam, pandas, colorama, pyyaml, filelock, funcsigs, protobuf, redis, py, more-itertools, atomicwrites, pluggy, pytest, click, ray, modin, bdgenomics.mango.pileup, psutil, jupyter-latex-envs, jupyter-highlight-selected-word, jupyter-contrib-core, jupyter-nbextensions-configurator, lxml, jupyter-contrib-nbextensions
  Found existing installation: prompt-toolkit 3.0.18
    Uninstalling prompt-toolkit-3.0.18:
      Successfully uninstalled prompt-toolkit-3.0.18
  Found existing installation: ipython 7.16.1
    Uninstalling ipython-7.16.1:
      Successfully uninstalled ipython-7.16.1
Successfully installed atomicwrites-1.4.0 bdgenomics.adam-0.34.0 bdgenomics.mango.pileup-0.0.6a0 cigar-0.1.3 click-7.1.2 colorama-0.4.4 cycler-0.10.0 filelock-3.0.12 funcsigs-1.0.2 ipython-7.8.0 ipywidgets-7.0.0 jupyter-1.0.0 jupyter-console-6.4.0 jupyter-contrib-core-0.3.3 jupyter-contrib-nbextensions-0.5.1 jupyter-highlight-selected-word-0.2.0 jupyter-latex-envs-1.4.6 jupyter-nbextensions-configurator-0.4.1 lxml-4.6.3 matplotlib-2.0.2 modin-0.6.1 more-itertools-8.7.0 numpy-1.19.5 pandas-0.25.1 pluggy-0.13.1 prompt-toolkit-2.0.10 protobuf-3.15.8 psutil-5.8.0 py-1.10.0 py4j-0.10.9 pyspark-3.1.1 pytest-3.9.1 pytz-2021.1 pyyaml-5.4.1 qtconsole-5.1.0 qtpy-1.9.0 ray-0.7.3 redis-3.5.3 widgetsnbextension-3.0.8
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded /home
+ popd
+ mvn -U -P python,distribution package -DskipTests -Dhadoop.version=3.2.1 -Dspark.version=3.0.1
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-core-spark3_2.12:jar:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-core-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/pom.xml, line 11, column 15
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-parent-spark3_${scala.version.prefix}:0.0.6-SNAPSHOT, /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/pom.xml, line 13, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-python-spark3_2.12:jar:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-python-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-python/pom.xml, line 11, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli-spark3_2.12:jar:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-cli-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-cli/pom.xml, line 11, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-assembly-spark3_2.12:jar:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-assembly-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/pom.xml, line 11, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-distribution-spark3_2.12:pom:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-distribution-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/pom.xml, line 11, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-parent-spark3_2.12:pom:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-parent-spark3_${scala.version.prefix}:0.0.6-SNAPSHOT, /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/pom.xml, line 13, column 15
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango_2.12: CORE                                                   [jar]
[INFO] Mango_2.12: Python APIs                                            [jar]
[INFO] mango_2.12: CLI                                                    [jar]
[INFO] Mango_2.12: Assembly                                               [jar]
[INFO] mango_2.12: Distribution                                           [pom]
[INFO] mango_2.12                                                         [pom]
[INFO] 
[INFO] ------------< org.bdgenomics.mango:mango-core-spark3_2.12 >-------------
[INFO] Building mango_2.12: CORE 0.0.6-SNAPSHOT                           [1/6]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core-spark3_2.12 ---
[INFO] Modified 0 of 32 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ mango-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] skip non existing resourceDirectory /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:compile (scala-compile-first) @ mango-core-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiler bridge file: /home/jenkins/.sbt/1.0/zinc/org.scala-sbt/org.scala-sbt-compiler-bridge_2.12-1.4.4-bin_2.12.10__52.0-1.4.4_20201220T223045.jar
[INFO] compile in 3.0 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ mango-core-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core-spark3_2.12 ---
[INFO] Test Source directory: /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:testResources (default-testResources) @ mango-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-core-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiler bridge file: /home/jenkins/.sbt/1.0/zinc/org.scala-sbt/org.scala-sbt-compiler-bridge_2.12-1.4.4-bin_2.12.10__52.0-1.4.4_20201220T223045.jar
[INFO] compiling 14 Scala sources to /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/scala-2.12.10/test-classes ...
[WARNING] /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala/org/bdgenomics/mango/io/HttpDownloadUtilitySuite.scala:23: imported `HttpDownloadUtility' is permanently hidden by definition of object HttpDownloadUtility in package io
[WARNING] /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala/org/bdgenomics/mango/models/FeatureMaterializationSuite.scala:54: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING] /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala/org/bdgenomics/mango/models/FeatureMaterializationSuite.scala:72: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING] /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala/org/bdgenomics/mango/models/FeatureMaterializationSuite.scala:73: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING] four warnings found
[INFO] done compiling
[INFO] compile in 11.1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ mango-core-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.2:test (test) @ mango-core-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ mango-core-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar-no-fork (attach-sources) @ mango-core-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.2.0:jar (attach-javadocs) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) > generate-sources @ mango-core-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) < generate-sources @ mango-core-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) @ mango-core-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
model contains 41 documentable templates
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:55: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                  ^
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:55: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                                    ^
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:56: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz
                                                                                   ^
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:57: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - refSeq.txt file: downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                 ^
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/RefSeq.scala:29: warning: Variable GENOME undefined in comment for object RefSeqFile in object RefSeqFile
 * Processes refSeq file, downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                     ^
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/io/HttpDownloadUtility.scala:34: warning: Could not find any member to link for "IOException".
  /**
  ^
6 warnings found
[INFO] Building jar: /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -----------< org.bdgenomics.mango:mango-python-spark3_2.12 >------------
[INFO] Building Mango_2.12: Python APIs 0.0.6-SNAPSHOT                    [2/6]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-python-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-python-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-python-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ mango-python-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] skip non existing resourceDirectory /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:compile (scala-compile-first) @ mango-python-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (dev-python) @ mango-python-spark3_2.12 ---
pip install -e .
Obtaining file:///tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-python
Requirement already satisfied: cigar==0.1.3 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (0.1.3)
Requirement already satisfied: matplotlib==2.0.2 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (2.0.2)
Requirement already satisfied: ipython==7.8.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (7.8.0)
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (1.0.0)
Requirement already satisfied: bdgenomics.adam==0.34.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (0.34.0)
Requirement already satisfied: bdgenomics.mango.pileup==0.0.6a0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (0.0.6a0)
Requirement already satisfied: ipywidgets==7.0.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (7.0.0)
Requirement already satisfied: psutil in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (5.8.0)
Requirement already satisfied: pytest==3.9.1 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (3.9.1)
Requirement already satisfied: jupyter_contrib_nbextensions in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (0.5.1)
Requirement already satisfied: pytz in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (2021.1)
Requirement already satisfied: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (2.4.7)
Requirement already satisfied: cycler>=0.10 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (0.10.0)
Requirement already satisfied: numpy>=1.7.1 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (1.19.5)
Requirement already satisfied: six>=1.10 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (1.16.0)
Requirement already satisfied: python-dateutil in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (2.8.1)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (49.6.0.post20210108)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (4.8.0)
Requirement already satisfied: pickleshare in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.7.5)
Requirement already satisfied: traitlets>=4.2 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (4.3.3)
Requirement already satisfied: backcall in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.2.0)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.17.2)
Requirement already satisfied: decorator in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (5.0.7)
Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (2.0.10)
Requirement already satisfied: pygments in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (2.9.0)
Requirement already satisfied: ipykernel in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (5.5.4)
Requirement already satisfied: jupyter-console in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (6.4.0)
Requirement already satisfied: nbconvert in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (6.0.7)
Requirement already satisfied: notebook in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (6.3.0)
Requirement already satisfied: qtconsole in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (5.1.0)
Requirement already satisfied: pyspark>=1.6.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.adam==0.34.0->bdgenomics.mango==0.0.6a2) (3.1.1)
Requirement already satisfied: modin[ray]==0.6.1 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (0.6.1)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (5.1.3)
Requirement already satisfied: widgetsnbextension~=3.0.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (3.0.8)
Requirement already satisfied: pluggy>=0.7 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango==0.0.6a2) (0.13.1)
Requirement already satisfied: atomicwrites>=1.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango==0.0.6a2) (1.4.0)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango==0.0.6a2) (20.3.0)
Requirement already satisfied: more-itertools>=4.0.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango==0.0.6a2) (8.7.0)
Requirement already satisfied: py>=1.5.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango==0.0.6a2) (1.10.0)
Requirement already satisfied: ipython-genutils in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter_contrib_nbextensions->bdgenomics.mango==0.0.6a2) (0.2.0)
Requirement already satisfied: lxml in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter_contrib_nbextensions->bdgenomics.mango==0.0.6a2) (4.6.3)
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Requirement already satisfied: jupyter-core in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jupyter_contrib_nbextensions->bdgenomics.mango==0.0.6a2) (4.7.1)
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Requirement already satisfied: wcwidth in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.2.5)
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Requirement already satisfied: nbclient<0.6.0,>=0.5.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.5.3)
Requirement already satisfied: jinja2>=2.4 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (2.11.3)
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Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.4.2)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.8.4)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.3)
Requirement already satisfied: bleach in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (3.3.0)
Requirement already satisfied: testpath in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.4.4)
Requirement already satisfied: jupyterlab-pygments in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.1.2)
Requirement already satisfied: prometheus-client in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.10.1)
Requirement already satisfied: Send2Trash>=1.5.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.5.0)
Requirement already satisfied: terminado>=0.8.3 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.9.4)
Requirement already satisfied: argon2-cffi in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (20.1.0)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (22.0.3)
Requirement already satisfied: qtpy in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.9.0)
Requirement already satisfied: py4j==0.10.9 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from pyspark>=1.6.0->bdgenomics.adam==0.34.0->bdgenomics.mango==0.0.6a2) (0.10.9)
Requirement already satisfied: pandas==0.25.1 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (0.25.1)
Requirement already satisfied: ray==0.7.3; extra == "ray" in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (0.7.3)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (3.2.0)
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from pluggy>=0.7->pytest==3.9.1->bdgenomics.mango==0.0.6a2) (4.0.1)
Requirement already satisfied: nest-asyncio in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.5.1)
Requirement already satisfied: async-generator in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.10)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jinja2>=2.4->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.1.1)
Requirement already satisfied: packaging in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (20.9)
Requirement already satisfied: webencodings in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.5.1)
Requirement already satisfied: cffi>=1.0.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.14.5)
Requirement already satisfied: funcsigs in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (1.0.2)
Requirement already satisfied: colorama in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (0.4.4)
Requirement already satisfied: protobuf>=3.8.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (3.15.8)
Requirement already satisfied: redis in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (3.5.3)
Requirement already satisfied: click in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (7.1.2)
Requirement already satisfied: filelock in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (3.0.12)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (0.17.3)
Requirement already satisfied: typing-extensions>=3.6.4; python_version < "3.8" in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pluggy>=0.7->pytest==3.9.1->bdgenomics.mango==0.0.6a2) (3.7.4.3)
Requirement already satisfied: zipp>=0.5 in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pluggy>=0.7->pytest==3.9.1->bdgenomics.mango==0.0.6a2) (3.4.1)
Requirement already satisfied: pycparser in /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (2.20)
Installing collected packages: bdgenomics.mango
  Running setup.py develop for bdgenomics.mango
Successfully installed bdgenomics.mango
python setup.py sdist bdist_egg
running sdist
running egg_info
writing bdgenomics.mango.egg-info/PKG-INFO
writing dependency_links to bdgenomics.mango.egg-info/dependency_links.txt
writing requirements to bdgenomics.mango.egg-info/requires.txt
writing top-level names to bdgenomics.mango.egg-info/top_level.txt
reading manifest file 'bdgenomics.mango.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no files found matching '*.jar' under directory 'deps/jars'
writing manifest file 'bdgenomics.mango.egg-info/SOURCES.txt'
running check
creating bdgenomics.mango-0.0.6a2
creating bdgenomics.mango-0.0.6a2/bdgenomics
creating bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
creating bdgenomics.mango-0.0.6a2/bdgenomics/mango
creating bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying files to bdgenomics.mango-0.0.6a2...
copying MANIFEST.in -> bdgenomics.mango-0.0.6a2
copying README.md -> bdgenomics.mango-0.0.6a2
copying requirements.txt -> bdgenomics.mango-0.0.6a2
copying setup.py -> bdgenomics.mango-0.0.6a2
copying version.py -> bdgenomics.mango-0.0.6a2
copying bdgenomics/__init__.py -> bdgenomics.mango-0.0.6a2/bdgenomics
copying bdgenomics.mango.egg-info/PKG-INFO -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/SOURCES.txt -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/dependency_links.txt -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/requires.txt -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/top_level.txt -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics/mango/__init__.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/alignments.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/coverage.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/distribution.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/features.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/genotypes.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/utils.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/variants.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/test/__init__.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/alignment_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/coverage_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/distribution_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/feature_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/genotypes_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/notebook_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/variant_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
Writing bdgenomics.mango-0.0.6a2/setup.cfg
creating dist
Creating tar archive
removing 'bdgenomics.mango-0.0.6a2' (and everything under it)
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/mango
copying bdgenomics/mango/utils.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/genotypes.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/coverage.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/__init__.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/variants.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/distribution.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/features.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/alignments.py -> build/lib/bdgenomics/mango
creating build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/coverage_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/distribution_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/feature_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/alignment_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/__init__.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/variant_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/genotypes_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/notebook_test.py -> build/lib/bdgenomics/mango/test
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/utils.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/genotypes.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/distribution.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/features.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/genotypes_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/alignment_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/notebook_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/feature_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/variant_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/coverage_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/distribution_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/variants.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/coverage.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/alignments.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/utils.py to utils.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/genotypes.py to genotypes.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/distribution.py to distribution.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/features.py to features.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/genotypes_test.py to genotypes_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/alignment_test.py to alignment_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/notebook_test.py to notebook_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/feature_test.py to feature_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/variant_test.py to variant_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/coverage_test.py to coverage_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/distribution_test.py to distribution_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/variants.py to variants.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/coverage.py to coverage.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/alignments.py to alignments.cpython-36.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
bdgenomics.__pycache__.__init__.cpython-36: module references __path__
bdgenomics.mango.__pycache__.__init__.cpython-36: module references __path__
creating 'dist/bdgenomics.mango-0.0.6a2-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ mango-python-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:testResources (default-testResources) @ mango-python-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] skip non existing resourceDirectory /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-python/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-python-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (test-python) @ mango-python-spark3_2.12 ---
pushd ../example-files/notebooks \
	&& jupyter nbconvert --to python mango-python-coverage.ipynb \
	&& jupyter nbconvert --to python mango-python-alignment.ipynb \
	&& jupyter nbconvert --to python mango-pileup.ipynb \
	&& jupyter nbconvert --to python mango-python-variants.ipynb
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/example-files/notebooks /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-python
[NbConvertApp] Converting notebook mango-python-coverage.ipynb to python
[NbConvertApp] Converting notebook mango-python-alignment.ipynb to python
[NbConvertApp] Converting notebook mango-pileup.ipynb to python
[NbConvertApp] Converting notebook mango-python-variants.ipynb to python
mkdir -p target
export PYTHONPATH=/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python:/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/lib/py4j-0.10.9-src.zip:${PYTHONPATH} \
&& export PYSPARK_SUBMIT_ARGS="--jars ../mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar --driver-class-path ../mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar pyspark-shell" \
&& python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux -- Python 3.6.13, pytest-3.9.1, py-1.10.0, pluggy-0.13.1 -- /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/bin/python
cachedir: .pytest_cache
rootdir: /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-python, inifile:
collecting ... collected 25 items

bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_coverage_distribution PASSED [  4%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_fragment_distribution PASSED [  8%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution PASSED [ 12%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_maximal_bin_size PASSED [ 16%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_no_elements PASSED [ 20%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_mapq_distribution PASSED [ 24%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_visualize_alignments FAILED [ 28%]
bdgenomics/mango/test/coverage_test.py::CoverageTest::test_coverage_distribution PASSED [ 32%]
bdgenomics/mango/test/coverage_test.py::CoverageTest::test_example_coverage PASSED [ 36%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_cumulative_count_distribution PASSED [ 40%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_fail_on_invalid_sample PASSED [ 44%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_normalized_count_distribution PASSED [ 48%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_sampling PASSED [ 52%]
bdgenomics/mango/test/feature_test.py::FeatureTest::test_visualize_features FAILED [ 56%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeCallRatesDistribution PASSED [ 60%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeSummary PASSED [ 64%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_HetHomRatioDistribution PASSED [ 68%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistribution PASSED [ 72%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistributionSampling PASSED [ 76%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_visualize_genotypes FAILED [ 80%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_alignment_example FAILED [ 84%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_coverage_example FAILED [ 88%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_example FAILED [ 92%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_variants_example PASSED [ 96%]
bdgenomics/mango/test/variant_test.py::VariantTest::test_visualize_variants FAILED [100%]

=================================== FAILURES ===================================
___________________ AlignmentTest.test_visualize_alignments ____________________

self = <bdgenomics.mango.test.alignment_test.AlignmentTest testMethod=test_visualize_alignments>

    def test_visualize_alignments(self):
    
        # load file
        ac = ADAMContext(self.ss)
        testFile = self.resourceFile("small.sam")
    
        # read alignments
        reads = ac.loadAlignments(testFile)
    
        alignmentViz = AlignmentSummary(self.ss, ac, reads)
    
        contig = "16"
        start = 26472780
        end = 26482780
    
>       x = alignmentViz.viewPileup(contig, start, end)

bdgenomics/mango/test/alignment_test.py:42: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdgenomics.mango.alignments.AlignmentSummary object at 0x7f88d62f90b8>
contig = '16', start = 26472780, end = 26482780, reference = 'hg19'
label = 'Reads', multipleGroupNames = False, showPlot = True

    def viewPileup(self, contig, start, end, reference = 'hg19', label = "Reads", multipleGroupNames = False, showPlot = True):
        """
        Visualizes a portion of this AlignmentDataset in a scrollable pileup widget
    
        Args:
            :param contig: contig of locus to view
            :param start: start position of locus to view
            :param end: end position of locus to view
            :param reference: genome build. Default is hg19
            :param label: name of alignment track
            :param multipleGroupName: determines whether to different show tracks for each group name.
            If false, coalesces into one track.
            :param showPlot: Disables widget, used for testing. Default is true.
    
        Returns:
            pileup view for alignments
        """
        contig_trimmed, contig_full = formatContig(contig)
    
        # Filter Dataset
        filtered = self.dataset.transform(lambda r: r.filter(((r.referenceName == contig_full) | (r.referenceName == contig_trimmed))
                                                                   & (r.start < end) & (r.end > start) & (r.readMapped)))
    
        # convert to GA4GH JSON to be consumed by mango-pileup module
>       json_map = self.ac._jvm.org.bdgenomics.mango.converters.GA4GHutil.alignmentDatasetToJSON(filtered._jvmRdd,
                                                                                                   multipleGroupNames)
E       AttributeError: 'AlignmentDataset' object has no attribute '_jvmRdd'

bdgenomics/mango/alignments.py:167: AttributeError
_____________________ FeatureTest.test_visualize_features ______________________

self = <bdgenomics.mango.test.feature_test.FeatureTest testMethod=test_visualize_features>

    def test_visualize_features(self):
        # load file
        ac = ADAMContext(self.ss)
        testFile = self.resourceFile("smalltest.bed")
    
        # read features
        features = ac.loadFeatures(testFile)
    
        featureViz = FeatureSummary(ac, features)
    
        contig = "chrM"
        start = 1
        end = 2000
    
>       x = featureViz.viewPileup(contig, start, end)

bdgenomics/mango/test/feature_test.py:41: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdgenomics.mango.features.FeatureSummary object at 0x7f88d62f5748>
contig = 'chrM', start = 1, end = 2000, reference = 'hg19', label = 'Features'
showPlot = True

    def viewPileup(self, contig, start, end, reference = 'hg19', label = "Features", showPlot = True):
        """
        Visualizes a portion of this FeatureDataset in a scrollable pileup widget
    
        Args:
            :param contig: contig of locus to view
            :param start: start position of locus to view
            :param end: end position of locus to view
            reference: genome build. Default is hg19
            label: name of feature track
            showPlot: Disables widget, used for testing. Default is true.
    
        Returns:
            pileup view for features
        """
    
        contig_trimmed, contig_full = formatContig(contig)
    
        # Filter dataset
        filtered = self.dataset.transform(lambda r: r.filter(((r.referenceName == contig_full) | (r.referenceName == contig_trimmed))
                                                           & (r.start < end) & (r.end > start)))
    
        # convert to GA4GH JSON to be consumed by mango-pileup module
>       json = self.ac._jvm.org.bdgenomics.mango.converters.GA4GHutil.featureDatasetToJSON(filtered._jvmRdd)
E       AttributeError: 'FeatureDataset' object has no attribute '_jvmRdd'

bdgenomics/mango/features.py:75: AttributeError
____________________ GenotypesTest.test_visualize_genotypes ____________________

self = <bdgenomics.mango.test.genotypes_test.GenotypesTest testMethod=test_visualize_genotypes>

    def test_visualize_genotypes(self):
        # load file
        ac = ADAMContext(self.ss)
        testFile = self.resourceFile("genodata.v3.test.vcf")
    
        # read features
        genotypes = ac.loadGenotypes(testFile)
    
        gs =  GenotypeSummary(self.ss, ac, genotypes)
    
        contig = "chr22"
        start = 21079600
        end = 21079700
    
>       x = gs.viewPileup(contig, start, end)

bdgenomics/mango/test/genotypes_test.py:100: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdgenomics.mango.genotypes.GenotypeSummary object at 0x7f88d62eb278>
contig = 'chr22', start = 21079600, end = 21079700, reference = 'hg19'
label = 'Genotypes', showPlot = True

    def viewPileup(self, contig, start, end, reference = 'hg19', label = "Genotypes", showPlot = True):
        """
        Visualizes a portion of this GenotypeRDD in a scrollable pileup widget
    
        Args:
            :param contig: contig of locus to view
            :param start: start position of locus to view
            :param end: end position of locus to view
            reference: genome build. Default is hg19
            label: name of genotype track
            showPlot: Disables widget, used for testing. Default is true.
    
        Returns:
            pileup view for genotypes
        """
        contig_trimmed, contig_full = formatContig(contig)
    
        # Filter dataset
        filtered = self.genotypeDataset.transform(lambda r: r.filter(((r.referenceName == contig_full) | (r.referenceName == contig_trimmed))
                                                           & (r.start < end) & (r.end > start)))
    
        # convert to GA4GH JSON to be consumed by mango-pileup module
>       json = self.ac._jvm.org.bdgenomics.mango.converters.GA4GHutil.genotypeDatasetToJSON(filtered._jvmRdd)
E       AttributeError: 'GenotypeDataset' object has no attribute '_jvmRdd'

bdgenomics/mango/genotypes.py:139: AttributeError
_____________________ NotebookTest.test_alignment_example ______________________

self = <bdgenomics.mango.test.notebook_test.NotebookTest testMethod=test_alignment_example>

    def test_alignment_example(self):
        # these variables are read into mango-python.py
        spark = self.ss
        testMode = True
        alignmentFile = self.exampleFile("chr17.7500000-7515000.sam")
    
        # this file is converted from mango-python-alignment.ipynb in the Makefile
        testAlignmentFile = self.exampleFile("notebooks/mango-python-alignment.py")
>       exec(open(testAlignmentFile).read())

bdgenomics/mango/test/notebook_test.py:57: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   ModuleNotFoundError: No module named 'bdgenomics.adam.rdd'

<string>:26: ModuleNotFoundError
______________________ NotebookTest.test_coverage_example ______________________

self = <bdgenomics.mango.test.notebook_test.NotebookTest testMethod=test_coverage_example>

    def test_coverage_example(self):
        # these variables are read into mango-python.py
        spark = self.ss
        testMode = True
        alignmentFile = self.exampleFile("chr17.7500000-7515000.sam")
    
        # this file is converted from mango-python.coverage.ipynb in the Makefile
        testCoverageFile = self.exampleFile("notebooks/mango-python-coverage.py")
>       exec(open(testCoverageFile).read())

bdgenomics/mango/test/notebook_test.py:47: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   ModuleNotFoundError: No module named 'bdgenomics.adam.rdd'

<string>:26: ModuleNotFoundError
__________________________ NotebookTest.test_example ___________________________

self = <bdgenomics.mango.test.notebook_test.NotebookTest testMethod=test_example>

    def test_example(self):
        # these variables are read into mango-python.py
        spark = self.ss
        testMode = True
        alignmentFile = self.exampleFile("chr17.7500000-7515000.sam")
        variantFile = self.exampleFile("snv.chr17.7502100-7502500.vcf")
        genotypeFile = self.exampleFile("genodata.v3.vcf")
        featureFile = self.exampleFile("chr17.582500-594500.bed")
    
        # this file is converted from ipynb in make test
        testFile = self.exampleFile("notebooks/mango-pileup.py")
>       exec(open(testFile).read())

bdgenomics/mango/test/notebook_test.py:37: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
<string>:73: in <module>
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdgenomics.mango.alignments.AlignmentSummary object at 0x7f88d636fc50>
contig = '17', start = 7500000, end = 7500500, reference = 'hg19'
label = 'Reads', multipleGroupNames = False, showPlot = True

    def viewPileup(self, contig, start, end, reference = 'hg19', label = "Reads", multipleGroupNames = False, showPlot = True):
        """
        Visualizes a portion of this AlignmentDataset in a scrollable pileup widget
    
        Args:
            :param contig: contig of locus to view
            :param start: start position of locus to view
            :param end: end position of locus to view
            :param reference: genome build. Default is hg19
            :param label: name of alignment track
            :param multipleGroupName: determines whether to different show tracks for each group name.
            If false, coalesces into one track.
            :param showPlot: Disables widget, used for testing. Default is true.
    
        Returns:
            pileup view for alignments
        """
        contig_trimmed, contig_full = formatContig(contig)
    
        # Filter Dataset
        filtered = self.dataset.transform(lambda r: r.filter(((r.referenceName == contig_full) | (r.referenceName == contig_trimmed))
                                                                   & (r.start < end) & (r.end > start) & (r.readMapped)))
    
        # convert to GA4GH JSON to be consumed by mango-pileup module
>       json_map = self.ac._jvm.org.bdgenomics.mango.converters.GA4GHutil.alignmentDatasetToJSON(filtered._jvmRdd,
                                                                                                   multipleGroupNames)
E       AttributeError: 'AlignmentDataset' object has no attribute '_jvmRdd'

bdgenomics/mango/alignments.py:167: AttributeError
_____________________ VariantTest.test_visualize_variants ______________________

self = <bdgenomics.mango.test.variant_test.VariantTest testMethod=test_visualize_variants>

    def test_visualize_variants(self):
        # load file
        ac = ADAMContext(self.ss)
        testFile = self.resourceFile("bqsr1.vcf")
    
        variants = ac.loadVariants(testFile)
    
        variantViz = VariantSummary(ac, variants)
    
        contig = "chrM"
        start = 1
        end = 2000
    
>       x = variantViz.viewPileup(contig, start, end)

bdgenomics/mango/test/variant_test.py:40: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdgenomics.mango.variants.VariantSummary object at 0x7f88c51b1eb8>
contig = 'chrM', start = 1, end = 2000, reference = 'hg19', label = 'Variants'
showPlot = True

    def viewPileup(self, contig, start, end, reference = 'hg19', label = "Variants", showPlot = True):
        """
        Visualizes a portion of this VariantRDD in a scrollable pileup widget
    
        Args:
            :param contig: contig of locus to view
            :param start: start position of locus to view
            :param end: end position of locus to view
            reference: genome build. Default is hg19
            label: name of variant track
            showPlot: Disables widget, used for testing. Default is true.
    
        Returns:
            pileup view for variants
        """
        contig_trimmed, contig_full = formatContig(contig)
    
        # Filter RDD
        filtered = self.dataset.transform(lambda r: r.filter(((r.referenceName == contig_full) | (r.referenceName == contig_trimmed))
                                                           & (r.start < end) & (r.end > start)))
    
        # convert to GA4GH JSON to be consumed by mango-pileup module
>       json = self.ac._jvm.org.bdgenomics.mango.converters.GA4GHutil.variantDatasetToJSON(filtered._jvmRdd)
E       AttributeError: 'VariantDataset' object has no attribute '_jvmRdd'

bdgenomics/mango/variants.py:74: AttributeError
- generated xml file: /tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/mango-python/target/pytest-reports/tests.xml -
=============================== warnings summary ===============================
/home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290/lib/python3.6/site-packages/ipywidgets/widgets/widget.py:287: DeprecationWarning: Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator.
  warnings.warn("Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator.", DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/mangoTestKs6UuZr/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
============== 7 failed, 18 passed, 64 warnings in 72.68 seconds ===============
Makefile:89: recipe for target 'test' failed
make: *** [test] Error 1
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 2 (Exit value: 2)
    at org.apache.commons.exec.DefaultExecutor.executeInternal (DefaultExecutor.java:404)
    at org.apache.commons.exec.DefaultExecutor.execute (DefaultExecutor.java:166)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:804)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:751)
    at org.codehaus.mojo.exec.ExecMojo.execute (ExecMojo.java:313)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
    at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:498)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.12 0.0.6-SNAPSHOT:
[INFO] 
[INFO] mango_2.12: CORE ................................... SUCCESS [ 28.340 s]
[INFO] Mango_2.12: Python APIs ............................ FAILURE [01:24 min]
[INFO] mango_2.12: CLI .................................... SKIPPED
[INFO] Mango_2.12: Assembly ............................... SKIPPED
[INFO] mango_2.12: Distribution ........................... SKIPPED
[INFO] mango_2.12 ......................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:53 min
[INFO] Finished at: 2021-05-06T18:16:09Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:exec (test-python) on project mango-python-spark3_2.12: Command execution failed.: Process exited with an error: 2 (Exit value: 2) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :mango-python-spark3_2.12
clean_up
+ clean_up
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.

## Package Plan ##

  environment location: /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290


The following packages will be REMOVED:

  _libgcc_mutex-0.1-conda_forge
  _openmp_mutex-4.5-1_gnu
  argon2-cffi-20.1.0-py36h8f6f2f9_2
  async_generator-1.10-py_0
  attrs-20.3.0-pyhd3deb0d_0
  backcall-0.2.0-pyh9f0ad1d_0
  backports-1.0-py_2
  backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0
  bleach-3.3.0-pyh44b312d_0
  brotlipy-0.7.0-py36h8f6f2f9_1001
  ca-certificates-2021.4.13-h06a4308_1
  certifi-2020.12.5-py36h06a4308_0
  cffi-1.14.5-py36hc120d54_0
  chardet-4.0.0-py36h5fab9bb_1
  cryptography-3.4.7-py36hb60f036_0
  decorator-5.0.7-pyhd8ed1ab_0
  defusedxml-0.7.1-pyhd8ed1ab_0
  entrypoints-0.3-pyhd8ed1ab_1003
  icu-68.1-h2531618_0
  idna-2.10-pyh9f0ad1d_0
  importlib-metadata-4.0.1-py36h5fab9bb_0
  ipykernel-5.5.4-py36hcb3619a_0
  ipython-7.16.1-py36he448a4c_2
  ipython_genutils-0.2.0-py_1
  jedi-0.17.2-py36h5fab9bb_1
  jinja2-2.11.3-pyh44b312d_0
  json5-0.9.5-pyh9f0ad1d_0
  jsonschema-3.2.0-pyhd8ed1ab_3
  jupyter_client-6.1.12-pyhd8ed1ab_0
  jupyter_core-4.7.1-py36h5fab9bb_0
  jupyterlab-2.0.1-py_0
  jupyterlab_pygments-0.1.2-pyh9f0ad1d_0
  jupyterlab_server-1.2.0-py_0
  ld_impl_linux-64-2.35.1-hea4e1c9_2
  libffi-3.3-h58526e2_2
  libgcc-ng-9.3.0-h2828fa1_19
  libgomp-9.3.0-h2828fa1_19
  libsodium-1.0.18-h36c2ea0_1
  libstdcxx-ng-9.3.0-h6de172a_19
  libuv-1.40.0-h7b6447c_0
  markupsafe-1.1.1-py36h8f6f2f9_3
  mistune-0.8.4-py36h8f6f2f9_1003
  nbclient-0.5.3-pyhd8ed1ab_0
  nbconvert-6.0.7-py36h5fab9bb_3
  nbformat-5.1.3-pyhd8ed1ab_0
  ncurses-6.2-h58526e2_4
  nest-asyncio-1.5.1-pyhd8ed1ab_0
  nodejs-14.8.0-hda19d22_0
  notebook-6.3.0-py36h5fab9bb_0
  openssl-1.1.1k-h27cfd23_0
  packaging-20.9-pyh44b312d_0
  pandoc-2.12-h7f98852_0
  pandocfilters-1.4.2-py_1
  parso-0.7.1-pyh9f0ad1d_0
  pexpect-4.8.0-pyh9f0ad1d_2
  pickleshare-0.7.5-py_1003
  pip-19.3.1-py36_0
  prometheus_client-0.10.1-pyhd8ed1ab_0
  prompt-toolkit-3.0.18-pyha770c72_0
  ptyprocess-0.7.0-pyhd3deb0d_0
  pycparser-2.20-pyh9f0ad1d_2
  pygments-2.9.0-pyhd8ed1ab_0
  pyopenssl-20.0.1-pyhd8ed1ab_0
  pyparsing-2.4.7-pyh9f0ad1d_0
  pyrsistent-0.17.3-py36h8f6f2f9_2
  pysocks-1.7.1-py36h5fab9bb_3
  python-3.6.13-hffdb5ce_0_cpython
  python-dateutil-2.8.1-py_0
  python_abi-3.6-1_cp36m
  pyzmq-22.0.3-py36h7068817_1
  readline-8.1-h46c0cb4_0
  requests-2.25.1-pyhd3deb0d_0
  send2trash-1.5.0-py_0
  setuptools-49.6.0-py36h5fab9bb_3
  six-1.16.0-pyh6c4a22f_0
  sqlite-3.35.5-h74cdb3f_0
  terminado-0.9.4-py36h5fab9bb_0
  testpath-0.4.4-py_0
  tk-8.6.10-h21135ba_1
  tornado-6.1-py36h8f6f2f9_1
  traitlets-4.3.3-py36h9f0ad1d_1
  typing_extensions-3.7.4.3-py_0
  urllib3-1.26.4-pyhd8ed1ab_0
  wcwidth-0.2.5-pyh9f0ad1d_2
  webencodings-0.5.1-py_1
  wheel-0.36.2-pyhd3deb0d_0
  xz-5.2.5-h516909a_1
  zeromq-4.3.4-h9c3ff4c_0
  zipp-3.4.1-pyhd8ed1ab_0
  zlib-1.2.11-h516909a_1010


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

Remove all packages in environment /home/jenkins/.conda/envs/mango-build-aa2884c0-7a4d-4ac8-a326-decba55ef290:

Build step 'Execute shell' marked build as failure
Finished: FAILURE