simple	23-Mar-2018 13:56:50	Build Clowder - extractors-plantcv - Default Job #27 (CATS-PLANTCV-JOB1-27) started building on agent buildserver-1.os.ncsa.edu
simple	23-Mar-2018 13:56:50	Remote agent on host buildserver-1.os.ncsa.edu
simple	23-Mar-2018 13:56:50	Build working directory is /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1
simple	23-Mar-2018 13:56:50	Executing build Clowder - extractors-plantcv - Default Job #27 (CATS-PLANTCV-JOB1-27)
simple	23-Mar-2018 13:56:50	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	23-Mar-2018 13:56:50	Checking out into /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1
simple	23-Mar-2018 13:56:50	Updating source code to revision: 01b8acd3e7355d8862ee13b7085af25da02b2311
simple	23-Mar-2018 13:56:50	Fetching 'refs/heads/master' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-plantcv.git'. Will try to do a shallow fetch.
simple	23-Mar-2018 13:56:50	Warning: Permanently added '[127.0.0.1]:36856' (RSA) to the list of known hosts.
simple	23-Mar-2018 13:56:50	Checking out revision 01b8acd3e7355d8862ee13b7085af25da02b2311.
simple	23-Mar-2018 13:56:50	Already on 'master'
simple	23-Mar-2018 13:56:50	Updated source code to revision: 01b8acd3e7355d8862ee13b7085af25da02b2311
simple	23-Mar-2018 13:56:50	Finished task 'Checkout Default Repository' with result: Success
simple	23-Mar-2018 13:56:50	Running pre-build action: VCS Version Collector
simple	23-Mar-2018 13:56:51	Starting task 'docker build' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	23-Mar-2018 13:56:51	Beginning to execute external process for build 'Clowder - extractors-plantcv - Default Job #27 (CATS-PLANTCV-JOB1-27)'\n ... running command line: \n/bin/sh docker.sh\n ... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=master\nbamboo_capability_system_builder_command_npm_6=/home/bamboo/node-v6.9.1/bin/npm\nbamboo_capability_system_builder_command_buckminster_4_3=/home/bamboo/buckminster-4.3/buckminster\nbamboo_capability_system_builder_node_Node_js_v6_9_1=/home/bamboo/node-v6.9.1/bin/node\nbamboo_dependency_parent_0=CATS-PYC2-69\nbamboo_capability_system_builder_command_buckminster_4_2=/home/bamboo/buckminster-4.2/buckminster\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=master\nbamboo_repository_revision_number=01b8acd3e7355d8862ee13b7085af25da02b2311\nbamboo_repository_139362322_branch_name=master\nbamboo_resultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PLANTCV-JOB1-27\nbamboo_capability_system_builder_command_sphinx=/usr/bin/sphinx-build\nbamboo_build_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1\nbamboo_planRepository_1_name=extractors-plantcv\nbamboo_buildKey=CATS-PLANTCV-JOB1\nbamboo_capability_system_os=linux\nbamboo_shortPlanName=extractors-plantcv\nbamboo_planRepository_name=extractors-plantcv\nbamboo_buildNumber=27\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PLANTCV-JOB1-27\nbamboo_planRepository_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-plantcv.git\nbamboo_agentId=140673027\nbamboo_planName=Clowder - extractors-plantcv\nbamboo_shortPlanKey=PLANTCV\nbamboo_capability_system_builder_command_sbt_0_13=/home/bamboo/sbt-0.13.2/bin/sbt\nbamboo_capability_system_builder_node_Node_js_v0_10_28=/home/bamboo/node-v0.10.28/bin/node\nbamboo_shortJobKey=JOB1\nbamboo_planRepository_revision=01b8acd3e7355d8862ee13b7085af25da02b2311\nbamboo_buildTimeStamp=2018-03-23T13:56:49.532-05:00\nbamboo_repository_previous_revision_number=01b8acd3e7355d8862ee13b7085af25da02b2311\nbamboo_capability_system_builder_command_npm=/home/bamboo/node-v0.10.28/bin/npm\nbamboo_capability_system_builder_mvn2_Maven_2=/home/bamboo/apache-maven-2.2.1\nbamboo_planRepository_previousRevision=01b8acd3e7355d8862ee13b7085af25da02b2311\nbamboo_repository_139362322_name=extractors-plantcv\nbamboo_repository_git_branch=master\nbamboo_buildResultKey=CATS-PLANTCV-JOB1-27\nbamboo_repository_branch_name=master\nbamboo_buildPlanName=Clowder - extractors-plantcv - Default Job\nbamboo_repository_139362322_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-plantcv.git\nbamboo_planRepository_1_revision=01b8acd3e7355d8862ee13b7085af25da02b2311\nbamboo_capability_system_builder_command_python3=/usr/bin/python3\nbamboo_repository_139362322_git_username=\nbamboo_repository_name=extractors-plantcv\nbamboo_buildFailed=false\nbamboo_capability_system_docker_executable=/usr/bin/docker\nbamboo_capability_system_builder_command_grunt=/home/bamboo/node-v0.10.28/bin/grunt\nbamboo_planRepository_branch=master\nbamboo_agentWorkingDirectory=/home/bamboo/bamboo-agent-home/xml-data/build-dir\nbamboo_capability_system_git_executable=/usr/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=01b8acd3e7355d8862ee13b7085af25da02b2311\nbamboo_capability_system_builder_sbt_SBT_0_13_13=/home/bamboo/sbt-0.13.13\nbamboo_planRepository_branchDisplayName=master\nbamboo_capability_system_builder_command_phantomjs=/home/bamboo/phantomjs-1.9.8/bin/phantomjs\nbamboo_planRepository_1_type=bbserver\nbamboo_planRepository_branchName=master\nbamboo_capability_system_builder_command_python2_7=/usr/bin/python2.7\nbamboo_capability_system_hostname=buildserver-1\nbamboo_repository_139362322_git_branch=master\nbamboo_capability_system_jdk_JDK=/home/bamboo/jdk1.8.0_66\nbamboo_capability_system_software_mongo=/usr/bin/mongo\nbamboo_plan_storageTag=plan-139165731\nbamboo_hg_cache_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_capability_system_builder_command_casperjs=/home/bamboo/node-v0.10.28/bin/casperjs\nbamboo_capability_system_software_rabbitmq=/usr/sbin/rabbitmqctl\nbamboo_repository_139362322_previous_revision_number=01b8acd3e7355d8862ee13b7085af25da02b2311\nbamboo_capability_system_jdk_JDK_1_8_0_66=/home/bamboo/jdk1.8.0_66\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=bbserver\nbamboo_git_cache_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-plantcv.git\nbamboo_capability_system_builder_node_Node_js=/home/bamboo/node-v0.10.28/bin/node\nbamboo_capability_system_builder_ant_Ant=/home/bamboo/apache-ant-1.9.4\nbamboo_capability_system_builder_mvn3_Maven_3=/home/bamboo/apache-maven-3.3.9\nbamboo_tmp_directory=/home/bamboo/bamboo-agent-home/temp\nbamboo_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1\nbamboo_planKey=CATS-PLANTCV\nbamboo_planRepository_1_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-plantcv.git\nbamboo_planRepository_username=\nbamboo_repository_139362322_revision_number=01b8acd3e7355d8862ee13b7085af25da02b2311\nbamboo_capability_system_jdk_JDK_1_8=/home/bamboo/jdk1.8.0_66\nbamboo_capability_system_jdk_JDK_1_6=/home/bamboo/jdk1.6.0_41\nbamboo_capability_system_builder_command_mkcrx=/home/bamboo/mkcrx/mkcrx.sh\nbamboo_capability_system_jdk_JDK_1_7=/home/bamboo/jdk1.7.0_60\nbamboo_planRepository_1_branchName=master\n
build	23-Mar-2018 13:56:51	Sending build context to Docker daemon 13.55 MB
build	23-Mar-2018 13:56:51	
build	23-Mar-2018 13:56:51	Step 1/21 : FROM clowder/pyclowder:1
build	23-Mar-2018 13:56:51	 ---> d1a9e970ed30
build	23-Mar-2018 13:56:51	Step 2/21 : MAINTAINER Max Burnette <mburnet2@illinois.edu>"
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 0f25af9aca3d
build	23-Mar-2018 13:56:51	Step 3/21 : ENV CLOWDER_HOME "/home/clowder" RABBITMQ_URI "" RABBITMQ_EXCHANGE "clowder" RABBITMQ_VHOST "%2F" RABBITMQ_QUEUE "terra.plantcv" MAIN_SCRIPT "extractors-plantcv.py"
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 3a809719a3e1
build	23-Mar-2018 13:56:51	Step 4/21 : USER root
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 0b62dd3f7d68
build	23-Mar-2018 13:56:51	Step 5/21 : RUN apt-get -y update &&         apt-get install -y -q build-essential &&         apt-get install -y -q wget git imagemagick             unzip cmake libgtk2.0-dev             python-dev python-numpy python-gtk2 python-matplotlib python-pip             libavcodec-dev libavformat-dev libswscale-dev libdc1394-22             libjpeg-dev libpng-dev libjasper-dev libtiff-dev libtbb-dev sqlite3 &&         rm -rf /var/lib/apt/lists/*
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 9699d4d1298b
build	23-Mar-2018 13:56:51	Step 6/21 : USER clowder
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 16933ffd0823
build	23-Mar-2018 13:56:51	Step 7/21 : RUN cd ${CLOWDER_HOME} &&     mkdir software &&     cd ${CLOWDER_HOME}/software &&     git clone -q https://github.com/Itseez/opencv.git &&     cd opencv && git checkout -q 2.4.8 &&     mkdir build && cd build &&     cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=${CLOWDER_HOME}/opencv -D WITH_TBB=ON -D BUILD_NEW_PYTHON_SUPPORT=ON .. &&     make && make install &&     cd ${CLOWDER_HOME}/software && rm -fr opencv
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 4907c52c60a6
build	23-Mar-2018 13:56:51	Step 8/21 : RUN cd ${CLOWDER_HOME} &&     mkdir -p plantcv-output &&     git clone https://github.com/danforthcenter/plantcv.git
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> c004532d24ec
build	23-Mar-2018 13:56:51	Step 9/21 : ENV PYTHONPATH "${CLOWDER_HOME}/opencv/lib/python2.7/dist-packages:${CLOWDER_HOME}/plantcv/lib:/usr/lib/python2.7/dist-packages:${PYTHONPATH}"
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 6fd825d34ba5
build	23-Mar-2018 13:56:51	Step 10/21 : ENV PATH "${CLOWDER_HOME}/opencv/bin:${PATH}"
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 465c2120f641
build	23-Mar-2018 13:56:51	Step 11/21 : ENV LD_LIBRARY_PATH "${CLOWDER_HOME}/opencv/lib:${LD_LIBRARY_PATH}"
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 2603f9998141
build	23-Mar-2018 13:56:51	Step 12/21 : USER root
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> b887034feca4
build	23-Mar-2018 13:56:51	Step 13/21 : RUN apt-get -y update &&     apt-get install -y python-opencv opencv-data
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> d29e459be8d2
build	23-Mar-2018 13:56:51	Step 14/21 : COPY requirements.txt /home/clowder/
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 8f2f4bb55535
build	23-Mar-2018 13:56:51	Step 15/21 : RUN cd ${CLOWDER_HOME} &&     pip install --upgrade pip &&     pip install -r /home/clowder/requirements.txt
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 4741915a8182
build	23-Mar-2018 13:56:51	Step 16/21 : USER clowder
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 39ec9b15b090
build	23-Mar-2018 13:56:51	Step 17/21 : COPY entrypoint.sh *.py *.json /home/clowder/
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 78f4530b804d
build	23-Mar-2018 13:56:51	Step 18/21 : RUN mkdir /home/clowder/bin
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 7055c38a6332
build	23-Mar-2018 13:56:51	Step 19/21 : COPY bin /home/clowder/bin
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 182f5b8c7cd9
build	23-Mar-2018 13:56:51	Step 20/21 : ENTRYPOINT /home/clowder/entrypoint.sh
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> 6a29c33fc719
build	23-Mar-2018 13:56:51	Step 21/21 : CMD extractor
build	23-Mar-2018 13:56:51	 ---> Using cache
build	23-Mar-2018 13:56:51	 ---> cab193d59f35
build	23-Mar-2018 13:56:51	Successfully built cab193d59f35
build	23-Mar-2018 13:56:51	The push refers to a repository [docker.io/clowder/extractors-plantcv]
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build	23-Mar-2018 13:56:53	browndog_v0.2.0: digest: sha256:1668fa06c4e94a02c309f71c262747118d67ff2e23bdd5b60ea1bd0e8d64d2ba size: 4085
build	23-Mar-2018 13:56:53	The push refers to a repository [docker.io/clowder/extractors-plantcv]
build	23-Mar-2018 13:56:53	c51508412f11: Preparing
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build	23-Mar-2018 13:56:54	The push refers to a repository [docker.io/clowder/extractors-plantcv]
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build	23-Mar-2018 13:56:54	0cdb02ac1d86: Waiting
build	23-Mar-2018 13:56:54	f2297bdfc824: Waiting
build	23-Mar-2018 13:56:54	0fbe2bcb1bf9: Waiting
build	23-Mar-2018 13:56:54	59669fcdd5eb: Waiting
build	23-Mar-2018 13:56:54	56cce883f669: Waiting
build	23-Mar-2018 13:56:54	7f7a065d245a: Waiting
build	23-Mar-2018 13:56:54	f96e6b25195f: Waiting
build	23-Mar-2018 13:56:54	ae620432889d: Waiting
build	23-Mar-2018 13:56:54	a2022691bf95: Waiting
build	23-Mar-2018 13:56:54	c56153825175: Waiting
build	23-Mar-2018 13:56:54	8a2699cc3040: Waiting
build	23-Mar-2018 13:56:54	f59b0ecb78a5: Waiting
build	23-Mar-2018 13:56:54	3f209317d601: Waiting
build	23-Mar-2018 13:56:55	5468b643779a: Layer already exists
build	23-Mar-2018 13:56:55	19b4bb0179a3: Layer already exists
build	23-Mar-2018 13:56:55	e168d44c8c4e: Layer already exists
build	23-Mar-2018 13:56:55	cc426dc25371: Layer already exists
build	23-Mar-2018 13:56:55	c51508412f11: Layer already exists
build	23-Mar-2018 13:56:55	f59b0ecb78a5: Layer already exists
build	23-Mar-2018 13:56:55	0cdb02ac1d86: Layer already exists
build	23-Mar-2018 13:56:55	56cce883f669: Layer already exists
build	23-Mar-2018 13:56:55	3f209317d601: Layer already exists
build	23-Mar-2018 13:56:55	8a2699cc3040: Layer already exists
build	23-Mar-2018 13:56:55	f2297bdfc824: Layer already exists
build	23-Mar-2018 13:56:55	0fbe2bcb1bf9: Layer already exists
build	23-Mar-2018 13:56:55	59669fcdd5eb: Layer already exists
build	23-Mar-2018 13:56:55	7f7a065d245a: Layer already exists
build	23-Mar-2018 13:56:55	f96e6b25195f: Layer already exists
build	23-Mar-2018 13:56:55	c56153825175: Layer already exists
build	23-Mar-2018 13:56:55	ae620432889d: Layer already exists
build	23-Mar-2018 13:56:55	a2022691bf95: Layer already exists
build	23-Mar-2018 13:56:56	latest: digest: sha256:1668fa06c4e94a02c309f71c262747118d67ff2e23bdd5b60ea1bd0e8d64d2ba size: 4085
build	23-Mar-2018 13:56:56	Untagged: 20754:latest
simple	23-Mar-2018 13:56:56	Finished task 'docker build' with result: Success
simple	23-Mar-2018 13:56:56	Running post build plugin 'Docker Container Cleanup'
simple	23-Mar-2018 13:56:56	Running post build plugin 'NCover Results Collector'
simple	23-Mar-2018 13:56:56	Running post build plugin 'Clover Results Collector'
simple	23-Mar-2018 13:56:56	Running post build plugin 'npm Cache Cleanup'
simple	23-Mar-2018 13:56:56	Running post build plugin 'Artifact Copier'
simple	23-Mar-2018 13:56:56	Finalising the build...
simple	23-Mar-2018 13:56:56	Stopping timer.
simple	23-Mar-2018 13:56:56	Build CATS-PLANTCV-JOB1-27 completed.
simple	23-Mar-2018 13:56:56	Running on server: post build plugin 'NCover Results Collector'
simple	23-Mar-2018 13:56:56	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	23-Mar-2018 13:56:56	Running on server: post build plugin 'Clover Delta Calculator'
simple	23-Mar-2018 13:56:56	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	23-Mar-2018 13:56:56	All post build plugins have finished
simple	23-Mar-2018 13:56:56	Generating build results summary...
simple	23-Mar-2018 13:56:56	Saving build results to disk...
simple	23-Mar-2018 13:56:56	Logging substituted variables...
simple	23-Mar-2018 13:56:56	Indexing build results...
simple	23-Mar-2018 13:56:56	Finished building CATS-PLANTCV-JOB1-27.