Build: #27 was successful
Job: Default Job was successful
Build log
The build generated 254 lines of output. Download or view full build log.
| 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 |
| 23-Mar-2018 13:56:50 | Remote agent on host buildserver-1.os.ncsa.edu |
| 23-Mar-2018 13:56:50 | Build working directory is /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1 |
| 23-Mar-2018 13:56:50 | Executing build Clowder - extractors-plantcv - Default Job #27 (CATS-PLANTCV-JOB1-27) |
| 23-Mar-2018 13:56:50 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 23-Mar-2018 13:56:50 | Checking out into /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1 |
| 23-Mar-2018 13:56:50 | Updating source code to revision: 01b8acd3e7355d8862ee13b7085af25da02b2311 |
| 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. |
| 23-Mar-2018 13:56:50 | Warning: Permanently added '[127.0.0.1]:36856' (RSA) to the list of known hosts. |
| 23-Mar-2018 13:56:50 | Checking out revision 01b8acd3e7355d8862ee13b7085af25da02b2311. |
| 23-Mar-2018 13:56:50 | Already on 'master' |
| 23-Mar-2018 13:56:50 | Updated source code to revision: 01b8acd3e7355d8862ee13b7085af25da02b2311 |
| 23-Mar-2018 13:56:50 | Finished task 'Checkout Default Repository' with result: Success |
| 23-Mar-2018 13:56:50 | Running pre-build action: VCS Version Collector |
| 23-Mar-2018 13:56:51 | Starting task 'docker build' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' |
| 23-Mar-2018 13:56:51 | Beginning to execute external process for build 'Clowder - extractors-plantcv - Default Job #27 (CATS-PLANTCV-JOB1-27)' ... running command line: /bin/sh docker.sh ... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=master bamboo_capability_system_builder_command_npm_6=/home/bamboo/node-v6.9.1/bin/npm bamboo_capability_system_builder_command_buckminster_4_3=/home/bamboo/buckminster-4.3/buckminster bamboo_capability_system_builder_node_Node_js_v6_9_1=/home/bamboo/node-v6.9.1/bin/node bamboo_dependency_parent_0=CATS-PYC2-69 bamboo_capability_system_builder_command_buckminster_4_2=/home/bamboo/buckminster-4.2/buckminster bamboo_dependency_parent_total=1 bamboo_planRepository_1_branchDisplayName=master bamboo_repository_revision_number=01b8acd3e7355d8862ee13b7085af25da02b2311 bamboo_repository_139362322_branch_name=master bamboo_resultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PLANTCV-JOB1-27 bamboo_capability_system_builder_command_sphinx=/usr/bin/sphinx-build bamboo_build_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1 bamboo_planRepository_1_name=extractors-plantcv bamboo_buildKey=CATS-PLANTCV-JOB1 bamboo_capability_system_os=linux bamboo_shortPlanName=extractors-plantcv bamboo_planRepository_name=extractors-plantcv bamboo_buildNumber=27 bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PLANTCV-JOB1-27 bamboo_planRepository_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-plantcv.git bamboo_agentId=140673027 bamboo_planName=Clowder - extractors-plantcv bamboo_shortPlanKey=PLANTCV bamboo_capability_system_builder_command_sbt_0_13=/home/bamboo/sbt-0.13.2/bin/sbt bamboo_capability_system_builder_node_Node_js_v0_10_28=/home/bamboo/node-v0.10.28/bin/node bamboo_shortJobKey=JOB1 bamboo_planRepository_revision=01b8acd3e7355d8862ee13b7085af25da02b2311 bamboo_buildTimeStamp=2018-03-23T13:56:49.532-05:00 bamboo_repository_previous_revision_number=01b8acd3e7355d8862ee13b7085af25da02b2311 bamboo_capability_system_builder_command_npm=/home/bamboo/node-v0.10.28/bin/npm bamboo_capability_system_builder_mvn2_Maven_2=/home/bamboo/apache-maven-2.2.1 bamboo_planRepository_previousRevision=01b8acd3e7355d8862ee13b7085af25da02b2311 bamboo_repository_139362322_name=extractors-plantcv bamboo_repository_git_branch=master bamboo_buildResultKey=CATS-PLANTCV-JOB1-27 bamboo_repository_branch_name=master bamboo_buildPlanName=Clowder - extractors-plantcv - Default Job bamboo_repository_139362322_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-plantcv.git bamboo_planRepository_1_revision=01b8acd3e7355d8862ee13b7085af25da02b2311 bamboo_capability_system_builder_command_python3=/usr/bin/python3 bamboo_repository_139362322_git_username= bamboo_repository_name=extractors-plantcv bamboo_buildFailed=false bamboo_capability_system_docker_executable=/usr/bin/docker bamboo_capability_system_builder_command_grunt=/home/bamboo/node-v0.10.28/bin/grunt bamboo_planRepository_branch=master bamboo_agentWorkingDirectory=/home/bamboo/bamboo-agent-home/xml-data/build-dir bamboo_capability_system_git_executable=/usr/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=01b8acd3e7355d8862ee13b7085af25da02b2311 bamboo_capability_system_builder_sbt_SBT_0_13_13=/home/bamboo/sbt-0.13.13 bamboo_planRepository_branchDisplayName=master bamboo_capability_system_builder_command_phantomjs=/home/bamboo/phantomjs-1.9.8/bin/phantomjs bamboo_planRepository_1_type=bbserver bamboo_planRepository_branchName=master bamboo_capability_system_builder_command_python2_7=/usr/bin/python2.7 bamboo_capability_system_hostname=buildserver-1 bamboo_repository_139362322_git_branch=master bamboo_capability_system_jdk_JDK=/home/bamboo/jdk1.8.0_66 bamboo_capability_system_software_mongo=/usr/bin/mongo bamboo_plan_storageTag=plan-139165731 bamboo_hg_cache_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/_hg-repositories-cache bamboo_capability_system_builder_command_casperjs=/home/bamboo/node-v0.10.28/bin/casperjs bamboo_capability_system_software_rabbitmq=/usr/sbin/rabbitmqctl bamboo_repository_139362322_previous_revision_number=01b8acd3e7355d8862ee13b7085af25da02b2311 bamboo_capability_system_jdk_JDK_1_8_0_66=/home/bamboo/jdk1.8.0_66 bamboo_planRepository_1_username= bamboo_planRepository_type=bbserver bamboo_git_cache_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-plantcv.git bamboo_capability_system_builder_node_Node_js=/home/bamboo/node-v0.10.28/bin/node bamboo_capability_system_builder_ant_Ant=/home/bamboo/apache-ant-1.9.4 bamboo_capability_system_builder_mvn3_Maven_3=/home/bamboo/apache-maven-3.3.9 bamboo_tmp_directory=/home/bamboo/bamboo-agent-home/temp bamboo_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PLANTCV-JOB1 bamboo_planKey=CATS-PLANTCV bamboo_planRepository_1_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-plantcv.git bamboo_planRepository_username= bamboo_repository_139362322_revision_number=01b8acd3e7355d8862ee13b7085af25da02b2311 bamboo_capability_system_jdk_JDK_1_8=/home/bamboo/jdk1.8.0_66 bamboo_capability_system_jdk_JDK_1_6=/home/bamboo/jdk1.6.0_41 bamboo_capability_system_builder_command_mkcrx=/home/bamboo/mkcrx/mkcrx.sh bamboo_capability_system_jdk_JDK_1_7=/home/bamboo/jdk1.7.0_60 bamboo_planRepository_1_branchName=master |
| 23-Mar-2018 13:56:51 | Sending build context to Docker daemon 13.55 MB |
| 23-Mar-2018 13:56:51 | |
| 23-Mar-2018 13:56:51 | Step 1/21 : FROM clowder/pyclowder:1 |
| 23-Mar-2018 13:56:51 | ---> d1a9e970ed30 |
| 23-Mar-2018 13:56:51 | Step 2/21 : MAINTAINER Max Burnette <mburnet2@illinois.edu>" |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 0f25af9aca3d |
| 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" |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 3a809719a3e1 |
| 23-Mar-2018 13:56:51 | Step 4/21 : USER root |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 0b62dd3f7d68 |
| 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/* |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 9699d4d1298b |
| 23-Mar-2018 13:56:51 | Step 6/21 : USER clowder |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 16933ffd0823 |
| 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 |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 4907c52c60a6 |
| 23-Mar-2018 13:56:51 | Step 8/21 : RUN cd ${CLOWDER_HOME} && mkdir -p plantcv-output && git clone https://github.com/danforthcenter/plantcv.git |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> c004532d24ec |
| 23-Mar-2018 13:56:51 | Step 9/21 : ENV PYTHONPATH "${CLOWDER_HOME}/opencv/lib/python2.7/dist-packages:${CLOWDER_HOME}/plantcv/lib:/usr/lib/python2.7/dist-packages:${PYTHONPATH}" |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 6fd825d34ba5 |
| 23-Mar-2018 13:56:51 | Step 10/21 : ENV PATH "${CLOWDER_HOME}/opencv/bin:${PATH}" |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 465c2120f641 |
| 23-Mar-2018 13:56:51 | Step 11/21 : ENV LD_LIBRARY_PATH "${CLOWDER_HOME}/opencv/lib:${LD_LIBRARY_PATH}" |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 2603f9998141 |
| 23-Mar-2018 13:56:51 | Step 12/21 : USER root |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> b887034feca4 |
| 23-Mar-2018 13:56:51 | Step 13/21 : RUN apt-get -y update && apt-get install -y python-opencv opencv-data |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> d29e459be8d2 |
| 23-Mar-2018 13:56:51 | Step 14/21 : COPY requirements.txt /home/clowder/ |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 8f2f4bb55535 |
| 23-Mar-2018 13:56:51 | Step 15/21 : RUN cd ${CLOWDER_HOME} && pip install --upgrade pip && pip install -r /home/clowder/requirements.txt |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 4741915a8182 |
| 23-Mar-2018 13:56:51 | Step 16/21 : USER clowder |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 39ec9b15b090 |
| 23-Mar-2018 13:56:51 | Step 17/21 : COPY entrypoint.sh *.py *.json /home/clowder/ |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 78f4530b804d |
| 23-Mar-2018 13:56:51 | Step 18/21 : RUN mkdir /home/clowder/bin |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 7055c38a6332 |
| 23-Mar-2018 13:56:51 | Step 19/21 : COPY bin /home/clowder/bin |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 182f5b8c7cd9 |
| 23-Mar-2018 13:56:51 | Step 20/21 : ENTRYPOINT /home/clowder/entrypoint.sh |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> 6a29c33fc719 |
| 23-Mar-2018 13:56:51 | Step 21/21 : CMD extractor |
| 23-Mar-2018 13:56:51 | ---> Using cache |
| 23-Mar-2018 13:56:51 | ---> cab193d59f35 |
| 23-Mar-2018 13:56:51 | Successfully built cab193d59f35 |
| 23-Mar-2018 13:56:51 | The push refers to a repository [docker.io/clowder/extractors-plantcv] |
| 23-Mar-2018 13:56:51 | c51508412f11: Preparing |
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| 23-Mar-2018 13:56:53 | browndog_v0.2.0: digest: sha256:1668fa06c4e94a02c309f71c262747118d67ff2e23bdd5b60ea1bd0e8d64d2ba size: 4085 |
| 23-Mar-2018 13:56:53 | The push refers to a repository [docker.io/clowder/extractors-plantcv] |
| 23-Mar-2018 13:56:53 | c51508412f11: Preparing |
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| 23-Mar-2018 13:56:54 | browndog_v0.3.0: digest: sha256:1668fa06c4e94a02c309f71c262747118d67ff2e23bdd5b60ea1bd0e8d64d2ba size: 4085 |
| 23-Mar-2018 13:56:54 | The push refers to a repository [docker.io/clowder/extractors-plantcv] |
| 23-Mar-2018 13:56:54 | c51508412f11: Preparing |
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| 23-Mar-2018 13:56:54 | 7f7a065d245a: Waiting |
| 23-Mar-2018 13:56:54 | f96e6b25195f: Waiting |
| 23-Mar-2018 13:56:54 | ae620432889d: Waiting |
| 23-Mar-2018 13:56:54 | a2022691bf95: Waiting |
| 23-Mar-2018 13:56:54 | c56153825175: Waiting |
| 23-Mar-2018 13:56:54 | 8a2699cc3040: Waiting |
| 23-Mar-2018 13:56:54 | f59b0ecb78a5: Waiting |
| 23-Mar-2018 13:56:54 | 3f209317d601: Waiting |
| 23-Mar-2018 13:56:55 | 5468b643779a: Layer already exists |
| 23-Mar-2018 13:56:55 | 19b4bb0179a3: Layer already exists |
| 23-Mar-2018 13:56:55 | e168d44c8c4e: Layer already exists |
| 23-Mar-2018 13:56:55 | cc426dc25371: Layer already exists |
| 23-Mar-2018 13:56:55 | c51508412f11: Layer already exists |
| 23-Mar-2018 13:56:55 | f59b0ecb78a5: Layer already exists |
| 23-Mar-2018 13:56:55 | 0cdb02ac1d86: Layer already exists |
| 23-Mar-2018 13:56:55 | 56cce883f669: Layer already exists |
| 23-Mar-2018 13:56:55 | 3f209317d601: Layer already exists |
| 23-Mar-2018 13:56:55 | 8a2699cc3040: Layer already exists |
| 23-Mar-2018 13:56:55 | f2297bdfc824: Layer already exists |
| 23-Mar-2018 13:56:55 | 0fbe2bcb1bf9: Layer already exists |
| 23-Mar-2018 13:56:55 | 59669fcdd5eb: Layer already exists |
| 23-Mar-2018 13:56:55 | 7f7a065d245a: Layer already exists |
| 23-Mar-2018 13:56:55 | f96e6b25195f: Layer already exists |
| 23-Mar-2018 13:56:55 | c56153825175: Layer already exists |
| 23-Mar-2018 13:56:55 | ae620432889d: Layer already exists |
| 23-Mar-2018 13:56:55 | a2022691bf95: Layer already exists |
| 23-Mar-2018 13:56:56 | latest: digest: sha256:1668fa06c4e94a02c309f71c262747118d67ff2e23bdd5b60ea1bd0e8d64d2ba size: 4085 |
| 23-Mar-2018 13:56:56 | Untagged: 20754:latest |
| 23-Mar-2018 13:56:56 | Finished task 'docker build' with result: Success |
| 23-Mar-2018 13:56:56 | Running post build plugin 'Docker Container Cleanup' |
| 23-Mar-2018 13:56:56 | Running post build plugin 'NCover Results Collector' |
| 23-Mar-2018 13:56:56 | Running post build plugin 'Clover Results Collector' |
| 23-Mar-2018 13:56:56 | Running post build plugin 'npm Cache Cleanup' |
| 23-Mar-2018 13:56:56 | Running post build plugin 'Artifact Copier' |
| 23-Mar-2018 13:56:56 | Finalising the build... |
| 23-Mar-2018 13:56:56 | Stopping timer. |
| 23-Mar-2018 13:56:56 | Build CATS-PLANTCV-JOB1-27 completed. |
| 23-Mar-2018 13:56:56 | Running on server: post build plugin 'NCover Results Collector' |
| 23-Mar-2018 13:56:56 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 23-Mar-2018 13:56:56 | Running on server: post build plugin 'Clover Delta Calculator' |
| 23-Mar-2018 13:56:56 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 23-Mar-2018 13:56:56 | All post build plugins have finished |
| 23-Mar-2018 13:56:56 | Generating build results summary... |
| 23-Mar-2018 13:56:56 | Saving build results to disk... |
| 23-Mar-2018 13:56:56 | Logging substituted variables... |
| 23-Mar-2018 13:56:56 | Indexing build results... |
| 23-Mar-2018 13:56:56 | Finished building CATS-PLANTCV-JOB1-27. |