FailedConsole Output

Skipping 1,687 KB.. Full Log
-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.0.0->ipywidgets>=6.0.0->bdgenomics.mango.pileup==0.0.3a0) (3.1.0)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.0.0->ipywidgets>=6.0.0->bdgenomics.mango.pileup==0.0.3a0) (0.3)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.0.0->ipywidgets>=6.0.0->bdgenomics.mango.pileup==0.0.3a0) (1.4.2)
Requirement already satisfied: mistune>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.0.0->ipywidgets>=6.0.0->bdgenomics.mango.pileup==0.0.3a0) (0.8.4)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.0.0->ipywidgets>=6.0.0->bdgenomics.mango.pileup==0.0.3a0) (0.4.2)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages (from bleach->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.0.0->ipywidgets>=6.0.0->bdgenomics.mango.pileup==0.0.3a0) (0.5.1)
Installing collected packages: bdgenomics.mango.pileup
  Found existing installation: bdgenomics.mango.pileup 0.0.2a0
    Uninstalling bdgenomics.mango.pileup-0.0.2a0:
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages/~dgenomics.mango.pileup-0.0.2a0.dist-info
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages/bdgenomics.mango.pileup-0.0.2a0.dist-info/
      Created temporary directory: /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/pip-uninstall-f529gmi0
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages/bdgenomics/__init__.py
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages/bdgenomics/~_pycache__
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages/bdgenomics/__pycache__/
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages/bdgenomics/~ango
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages/bdgenomics/mango/
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/share/jupyter/nbextensions/~ileup
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/share/jupyter/nbextensions/pileup/
      Successfully uninstalled bdgenomics.mango.pileup-0.0.2a0
  Running setup.py develop for bdgenomics.mango.pileup
    Running command /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/bin/python -c 'import setuptools, tokenize;__file__='"'"'/tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
    setup.py entered
    $PATH=/home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
    running develop
    running egg_info
    writing bdgenomics.mango.pileup.egg-info/PKG-INFO
    writing dependency_links to bdgenomics.mango.pileup.egg-info/dependency_links.txt
    writing requirements to bdgenomics.mango.pileup.egg-info/requires.txt
    writing top-level names to bdgenomics.mango.pileup.egg-info/top_level.txt
    reading manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    Could not import pypandoc - required to package bdgenomics.mango
    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 'version.py'
    warning: no files found matching '*.*' under directory 'pileup/static'
    writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    running build_ext
    Creating /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/lib/python3.6/site-packages/bdgenomics.mango.pileup.egg-link (link to .)
    Adding bdgenomics.mango.pileup 0.0.3a0 to easy-install.pth file

    Installed /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz
Successfully installed bdgenomics.mango.pileup
Cleaning up...
Removed build tracker '/tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-dfqj97m5'
jupyter nbextension enable --py widgetsnbextension
Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: OK
jupyter nbextension install --py --symlink --user bdgenomics.mango.pileup
Installing /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/pileup/static -> pileup
Symlinking: /home/jenkins/.local/share/jupyter/nbextensions/pileup -> /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/pileup/static
- Validating: OK

    To initialize this nbextension in the browser every time the notebook (or other app) loads:
    
          jupyter nbextension enable bdgenomics.mango.pileup --user --py
    
jupyter nbextension enable bdgenomics.mango.pileup --py --user
Enabling notebook extension pileup/extension...
      - Validating: OK
python setup.py sdist bdist_egg
setup.py entered
$PATH=/home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
running sdist
running egg_info
writing bdgenomics.mango.pileup.egg-info/PKG-INFO
writing dependency_links to bdgenomics.mango.pileup.egg-info/dependency_links.txt
writing requirements to bdgenomics.mango.pileup.egg-info/requires.txt
writing top-level names to bdgenomics.mango.pileup.egg-info/top_level.txt
reading manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
Could not import pypandoc - required to package bdgenomics.mango
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 'version.py'
warning: no files found matching '*.*' under directory 'pileup/static'
writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
running check
creating bdgenomics.mango.pileup-0.0.3a0
creating bdgenomics.mango.pileup-0.0.3a0/bdgenomics
creating bdgenomics.mango.pileup-0.0.3a0/bdgenomics.mango.pileup.egg-info
creating bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango
creating bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup
creating bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup/static
copying files to bdgenomics.mango.pileup-0.0.3a0...
copying MANIFEST.in -> bdgenomics.mango.pileup-0.0.3a0
copying README.md -> bdgenomics.mango.pileup-0.0.3a0
copying requirements.txt -> bdgenomics.mango.pileup-0.0.3a0
copying setup.py -> bdgenomics.mango.pileup-0.0.3a0
copying bdgenomics/__init__.py -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics
copying bdgenomics.mango.pileup.egg-info/PKG-INFO -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/SOURCES.txt -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/dependency_links.txt -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/not-zip-safe -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/requires.txt -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/top_level.txt -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics.mango.pileup.egg-info
copying bdgenomics/mango/__init__.py -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/pileup/__init__.py -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/_version.py -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/pileupViewer.py -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/sources.py -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/track.py -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/static/extension.js -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js.map -> bdgenomics.mango.pileup-0.0.3a0/bdgenomics/mango/pileup/static
Writing bdgenomics.mango.pileup-0.0.3a0/setup.cfg
creating dist
Creating tar archive
removing 'bdgenomics.mango.pileup-0.0.3a0' (and everything under it)
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
copying bdgenomics/mango/pileup/static/extension.js -> build/lib/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js -> build/lib/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js.map -> build/lib/bdgenomics/mango/pileup/static
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/mango
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/_version.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/track.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/pileupViewer.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/static/index.js -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/static/index.js.map -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/static/extension.js -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/sources.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/_version.py to _version.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/track.py to track.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/pileupViewer.py to pileupViewer.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/sources.py to sources.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/__init__.py to __init__.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/__init__.py to __init__.cpython-36.pyc
installing package data to build/bdist.linux-x86_64/egg
running install_data
creating build/bdist.linux-x86_64/egg/share
creating build/bdist.linux-x86_64/egg/share/jupyter
creating build/bdist.linux-x86_64/egg/share/jupyter/nbextensions
creating build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
copying bdgenomics/mango/pileup/static/extension.js -> build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
copying bdgenomics/mango/pileup/static/index.js -> build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
copying bdgenomics/mango/pileup/static/index.js.map -> build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/bdgenomics.mango.pileup-0.0.3a0-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:3.5.1:compile (default-compile) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-viz ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (test-python) @ mango-viz ---
pushd ../example-files/notebooks \
	&& jupyter nbconvert --to python mango-viz.ipynb
/tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/example-files/notebooks /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz
[NbConvertApp] Converting notebook mango-viz.ipynb to python
[NbConvertApp] Writing 1661 bytes to mango-viz.py
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics/mango/pileup/
============================= test session starts ==============================
platform linux -- Python 3.6.8, pytest-2.8.3, py-1.8.0, pluggy-0.3.1 -- /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/bin/python
cachedir: .cache
rootdir: /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz, inifile: 
collecting ... collected 19 items

bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_features PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_genes PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_genotypes PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_pileup PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_variants PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_embed_pileup PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_embed_data_two_widgets PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_snippet PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_minimal_pileup_html PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_coverage PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_features PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_genes PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_genome PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_location PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_pileup PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_scale PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_variants PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_serialization PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_tracks_serialization PASSED

- generated xml file: /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz/target/pytest-reports/tests.xml -
========================== 19 passed in 0.44 seconds ===========================
# run lint and flow for js
pushd bdgenomics/mango/js \
	&& npm run lint 
/tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz

> bdgenomics.mango.pileup@0.0.2-a0 lint /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js
> ./scripts/lint.sh

[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-viz ---
[INFO] Tests are skipped.
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  3.925 s]
[INFO] Mango: Python visualization hooks .................. SUCCESS [ 20.496 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 24.581 s
[INFO] Finished at: 2019-06-03T09:48:13-07:00
[INFO] Final Memory: 22M/1096M
[INFO] ------------------------------------------------------------------------
+ pushd mango-viz
/tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-viz /tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ make clean
rm -rf bdgenomics/mango/js/dist
rm -rf bdgenomics.mango.pileup.egg-info/
rm -rf bdgenomics/mango/pileup/static/
rm -rf dist/
rm -rf bdgenomics/mango/js/node_modules
jupyter nbextension uninstall pileup
Removing: /home/jenkins/.local/share/jupyter/nbextensions/pileup
+ popd
/tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ grep bdgenomics.mango
+ grep egg
+ tar tzvf mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.tar.gz
drwxr-xr-x 0/0                     0 2019-06-03 09:43 mango-distribution-0.0.3-SNAPSHOT/bdgenomics.mango.egg-info/
-rwxr-xr-x jenkins/jenkins        11 2019-06-03 09:43 mango-distribution-0.0.3-SNAPSHOT/bdgenomics.mango.egg-info/top_level.txt
-rwxr-xr-x jenkins/jenkins        46 2019-06-03 09:43 mango-distribution-0.0.3-SNAPSHOT/bdgenomics.mango.egg-info/dependency_links.txt
-rwxr-xr-x jenkins/jenkins       310 2019-06-03 09:43 mango-distribution-0.0.3-SNAPSHOT/bdgenomics.mango.egg-info/PKG-INFO
-rwxr-xr-x jenkins/jenkins       827 2019-06-03 09:43 mango-distribution-0.0.3-SNAPSHOT/bdgenomics.mango.egg-info/SOURCES.txt
-rwxr-xr-x jenkins/jenkins       143 2019-06-03 09:43 mango-distribution-0.0.3-SNAPSHOT/bdgenomics.mango.egg-info/requires.txt
-rw-r--r-- jenkins/jenkins     49263 2019-06-03 09:43 mango-distribution-0.0.3-SNAPSHOT/repo/bdgenomics.mango-0.0.3a0-py3.6.egg
-rw-r--r-- jenkins/jenkins     48582 2019-06-03 09:35 mango-distribution-0.0.3-SNAPSHOT/repo/bdgenomics.mango-0.0.3a0-py2.7.egg
+ MANGO_NOTEBOOK_LOGS=/tmp/mangoTestb2dyzRy/deleteMePleaseThisIsNoLongerNeeded/mango-notebook.log
+ sleep 2
+ bash -xv /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../bin/mango-notebook
+ kill 27072
+ echo 'Mango Notebook Succeeded'
Mango Notebook Succeeded
+ cp -r mango-python/target /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../mango-python/
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test: line 169: 27072 Terminated              bash -xv ${PROJECT_ROOT}/bin/mango-notebook &> ${MANGO_NOTEBOOK_LOGS}
+ source deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/bin

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
++ [[ -z /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ]]

if (( $? == 0 )); then
    # Inverse of activation: run deactivate scripts prior to deactivating env
    _CONDA_D="${CONDA_PREFIX}/etc/conda/deactivate.d"
    if [[ -d $_CONDA_D ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi

#    # get the activation path that would have been provided for this prefix
#    _LAST_ACTIVATE_PATH=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$CONDA_PREFIX")
#
#    # in activate, we replace a placeholder so that conda keeps its place in the PATH order
#    # The activate script sets _CONDA_HOLD here to activate that behavior.
#    #   Otherwise, PATH is simply removed.
#    if [ -n "$_CONDA_HOLD" ]; then
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'CONDA_PATH_PLACEHOLDER\1', '$PATH', 1))")"
#    else
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'', '$PATH', 1))")"
#    fi
#
#    unset _LAST_ACTIVATE_PATH

    export PATH=$("$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX")

    unset CONDA_DEFAULT_ENV
    unset CONDA_PREFIX
    unset CONDA_PATH_BACKUP
    export PS1="$CONDA_PS1_BACKUP"
    unset CONDA_PS1_BACKUP
    unset _CONDA_PYTHON2
else
    unset _CONDA_PYTHON2
    return $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6
++ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ unset CONDA_DEFAULT_ENV
++ unset CONDA_PREFIX
++ unset CONDA_PATH_BACKUP
++ export PS1=
++ PS1=
++ unset CONDA_PS1_BACKUP
++ unset _CONDA_PYTHON2

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ conda remove -y --name mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6 --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/mango-build-15a83840-1b68-4446-8430-9f5b512a9fc6:

The following packages will be REMOVED:

    ca-certificates: 2019.1.23-0            
    certifi:         2019.3.9-py36_0        
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       8.2.0-hdf63c60_1       
    libstdcxx-ng:    8.2.0-hdf63c60_1       
    ncurses:         6.1-he6710b0_1         
    nodejs:          10.13.0-he6710b0_0     
    openssl:         1.1.1c-h7b6447c_1      
    pip:             19.1.1-py36_0          
    python:          3.6.8-h0371630_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      41.0.1-py36_0          
    sqlite:          3.28.0-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.4-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-h7b6447c_3      

+ MANGO_BROWSER_LOGS=mango-submit.log
+ sleep 10
+ bash -xv /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../example-files/browser-scripts/run-example.sh
+ curl --header 'Content-type: application/json' --request POST --data '{"pageToken":null,"pageSize":200,"readGroupIds":["chr17_7500000-7515000_sam"],"referenceId":"chr17","start":1,"end":100}' http://localhost:8080/reads/search
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   165  100    45  100   120   3544   9451 --:--:-- --:--:-- --:--:-- 10909
{
  "alignments": [],
  "nextPageToken": ""
}+ curl --header 'Content-type: application/json' --request POST --data '{"variantSetId":"ALL_chr17_7500000-7515000_phase3_shapeit2_mvncall_integrated_v5a_20130502_genotypes_vcf","pageToken":null,"pageSize":400,"referenceName":"chr17","callSetIds":[],"start":7500000,"end":7515000}' http://localhost:8080/variants/search
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0{
  "variants": [{
    "id": "",
    "variantSetId": "",
    "names": ["rs78625018"],
    "created": "0",
    "updated": "0",
    "referenceName": "chr17",
    "start": "7500030",
    "end": "7500031",
    "referenceBases": "G",
    "alternateBases": ["A"],
    "calls": [{
      "callSetName": "HG00096",
      "callSetId": "HG00096",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00097",
      "callSetId": "HG00097",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00099",
      "callSetId": "HG00099",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00100",
      "callSetId": "HG00100",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00101",
      "callSetId": "HG00101",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }],
    "filtersApplied": false,
    "filtersPassed": true,
    "filtersFailed": [],
    "variantType": "",
    "svlen": "0",
    "cipos": [],
    "ciend": []
  }, {
    "id": "",
    "variantSetId": "",
    "names": ["rs568301902"],
    "created": "0",
    "updated": "0",
    "referenceName": "chr17",
    "start": "7514916",
    "end": "7514917",
    "referenceBases": "C",
    "alternateBases": ["T"],
    "calls": [{
      "callSetName": "HG00096",
      "callSetId": "HG00096",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00097",
      "callSetId": "HG00097",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00099",
      "callSetId": "HG00099",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00100",
      "callSetId": "HG00100",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00101",
      "callSetId": "HG00101",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }],
    "filtersApplied": false,
    "filtersPassed": true,
    "filtersFailed": [],
    "variantType": "",
    "svlen": "0",
    "cipos": [],
    "ciend": []
  }, {
    "id": "",
    "variantSetId": "",
    "names": ["rs546830486"],
    "created": "0",
    "updated": "0",
    "referenceName": "chr17",
    "start": "7514881",
    "end": "7514882",
    "referenceBases": "A",
    "alternateBases": ["G"],
    "calls": [{
      "callSetName": "HG00096",
      "callSetId": "HG00096",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00097",
      "callSetId": "HG00097",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00099",
      "callSetId": "HG00099",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00100",
      "callSetId": "HG00100",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00101",
      "callSetId": "HG00101",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }],
    "filtersApplied": false,
    "filtersPassed": true,
    "filtersFailed": [],
    "variantType": "",
    "svlen": "0",
    "cipos": [],
    "ciend": []
  }, {
    "id": "",
    "variantSetId": "",
    "names": ["rs555065313"],
    "created": "0",
    "updated": "0",
    "referenceName": "chr17",
    "start": "7514859",
    "end": "7514860",
    "referenceBases": "C",
    "alternateBases": ["T"],
    "calls": [{
      "callSetName": "HG00096",
      "callSetId": "HG00096",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00097",
      "callSetId": "HG00097",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00099",
      "callSetId": "HG00099",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00100",
      "callSetId": "HG00100",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00101",
      "callSetId": "HG00101",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }],
    "filtersApplied": false,
    "filtersPassed": true,
    "filtersFailed": [],
    "variantType": "",
    "svlen": "0",
    "cipos": [],
    "ciend": []
  }, {
    "id": "",
    "variantSetId": "",
    "names": ["rs146713658"],
    "created": "0",
    "updated": "0",
    "referenceName": "chr17",
    "start": "7514814",
    "end": "7514815",
    "referenceBases": "G",
    "alternateBases": ["A"],
    "calls": [{
      "callSetName": "HG00096",
      "callSetId": "HG00096",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00097",
      "callSetId": "HG00097",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00099",
      "callSetId": "HG00099",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00100",
      "callSetId": "HG00100",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00101",
      "callSetId": "HG00101",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }],
    "filtersApplied": false,
    "filtersPassed": true,
    "filtersFailed": [],
    "variantType": "",
    "svlen": "0",
    "cipos": [],
    "ciend": []
  }, {
    "id": "",
    "variantSetId": "",
    "names": ["rs546007412"],
    "created": "0",
    "updated": "0",
    "referenceName": "chr17",
    "start": "7514813",
    "end": "7514814",
    "referenceBases": "C",
    "alternateBases": ["T"],
    "calls": [{
      "callSetName": "HG00096",
      "callSetId": "HG00096",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00097",
      "callSetId": "HG00097",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00099",
      "callSetId": "HG00099",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00100",
      "callSetId": "HG00100",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00101",
      "callSetId": "HG00101",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }],
    "filtersApplied": false,
    "filtersPassed": true,
    "filtersFailed": [],
    "variantType": "",
    "svlen": "0",
    "cipos": [],
    "ciend": []
  }, {
    "id": "",
    "variantSetId": "",
    "names": ["rs551088664"],
    "created": "0",
    "updated": "0",
    "referenceName": "chr17",
    "start": "7514759",
    "end": "7514760",
    "referenceBases": "C",
    "alternateBases": ["T"],
    "calls": [{
      "callSetName": "HG00096",
      "callSetId": "HG00096",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00097",
      "callSetId": "HG00097",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00099",
      "callSetId": "HG00099",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00100",
      "callSetId": "HG00100",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00101",
      "callSetId": "HG00101",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }],
    "filtersApplied": false,
    "filtersPassed": true,
    "filtersFailed": [],
    "variantType": "",
    "svlen": "0",
    "cipos": [],
    "ciend": []
  }, {
    "id": "",
    "variantSetId": "",
    "names": ["rs143972836"],
    "created": "0",
    "updated": "0",
    "referenceName": "chr17",
    "start": "7514673",
    "end": "7514674",
    "referenceBases": "T",
    "alternateBases": ["G"],
    "calls": [{
      "callSetName": "HG00096",
      "callSetId": "HG00096",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00097",
      "callSetId": "HG00097",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00099",
      "callSetId": "HG00099",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00100",
      "callSetId": "HG00100",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }, {
      "callSetName": "HG00101",
      "callSetId": "HG00101",
      "phaseset": "",
      "genotypeLikelihood": [],
      "genotype": ["0", "0"]
    }],
    "filtersApplied": false,
    "filtersPassed": true,
    "filtersFailed": [],
    "variantType": "",
    "svlen": "0",
    "cipos": [],
    "ciend": []
  }, {
    "id": "",
    "variantSetId": "",
    "names": ["rs138501483"],
    "created": "0",
    "updated": "0",
    "referenceName": "chr17",
    "start": "7514606",
    "end": "7514607",
    "referenceBases": "C",
    "alternateBases": ["T"],
    "calls": [{
      "callSetName": "HG00096",
      "callSetId": "HG00096",
      "phaseset": "",
      "genotypeLikelihood": [],
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Build step 'Execute shell' marked build as failure
Finished: FAILURE