simple	18-Apr-2018 17:18:46	Build Clowder - extractors-msc - Default Job #35 (CATS-MSC-JOB1-35) started building on agent buildserver-1.os.ncsa.edu
simple	18-Apr-2018 17:18:46	Remote agent on host buildserver-1.os.ncsa.edu
simple	18-Apr-2018 17:18:46	Build working directory is /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC-JOB1
simple	18-Apr-2018 17:18:46	Executing build Clowder - extractors-msc - Default Job #35 (CATS-MSC-JOB1-35)
simple	18-Apr-2018 17:18:46	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	18-Apr-2018 17:18:46	Checking out into /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC-JOB1
simple	18-Apr-2018 17:18:46	Updating source code to revision: 6aaab3692bc88bb1c0016521723c45399615c5f2
simple	18-Apr-2018 17:18:46	Creating local git repository in '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC-JOB1/.git'.
simple	18-Apr-2018 17:18:46	Initialized empty Git repository in /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC-JOB1/.git/
simple	18-Apr-2018 17:18:47	Fetching 'refs/heads/master' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git'. Will try to do a shallow fetch.
simple	18-Apr-2018 17:18:47	Warning: Permanently added '[127.0.0.1]:34990' (RSA) to the list of known hosts.
simple	18-Apr-2018 17:18:49	From ssh://127.0.0.1:34990/cats/extractors-msc
simple	18-Apr-2018 17:18:49	 * [new branch]      master     -> master
simple	18-Apr-2018 17:18:49	 * [new tag]         browndog_v0.2.0 -> browndog_v0.2.0
simple	18-Apr-2018 17:18:49	 * [new tag]         browndog_v0.3.0 -> browndog_v0.3.0
simple	18-Apr-2018 17:18:49	Checking out revision 6aaab3692bc88bb1c0016521723c45399615c5f2.
simple	18-Apr-2018 17:18:49	Already on 'master'
simple	18-Apr-2018 17:18:49	Updated source code to revision: 6aaab3692bc88bb1c0016521723c45399615c5f2
simple	18-Apr-2018 17:18:49	Finished task 'Checkout Default Repository' with result: Success
simple	18-Apr-2018 17:18:49	Running pre-build action: VCS Version Collector
simple	18-Apr-2018 17:18:49	Starting task 'docker build' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	18-Apr-2018 17:18:49	Beginning to execute external process for build 'Clowder - extractors-msc - Default Job #35 (CATS-MSC-JOB1-35)'\n ... running command line: \n/bin/sh docker.sh\n ... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC-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-PYC2-70\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=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_resultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-MSC-JOB1-35\nbamboo_repository_127172627_branch_name=master\nbamboo_repository_127172627_git_branch=master\nbamboo_capability_system_builder_command_sphinx=/usr/bin/sphinx-build\nbamboo_build_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC-JOB1\nbamboo_planRepository_1_name=extractors-msc\nbamboo_buildKey=CATS-MSC-JOB1\nbamboo_capability_system_os=linux\nbamboo_shortPlanName=extractors-msc\nbamboo_planRepository_name=extractors-msc\nbamboo_repository_127172627_git_username=\nbamboo_buildNumber=35\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-MSC-JOB1-35\nbamboo_planRepository_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git\nbamboo_agentId=140673027\nbamboo_planName=Clowder - extractors-msc\nbamboo_repository_127172627_revision_number=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_shortPlanKey=MSC\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=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_buildTimeStamp=2018-04-18T16:45:43.152-05:00\nbamboo_repository_previous_revision_number=6aaab3692bc88bb1c0016521723c45399615c5f2\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=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_repository_git_branch=master\nbamboo_buildResultKey=CATS-MSC-JOB1-35\nbamboo_repository_branch_name=master\nbamboo_buildPlanName=Clowder - extractors-msc - Default Job\nbamboo_planRepository_1_revision=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_capability_system_builder_command_python3=/usr/bin/python3\nbamboo_repository_name=extractors-msc\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=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_capability_system_builder_sbt_SBT_0_13_13=/home/bamboo/sbt-0.13.13\nbamboo_repository_127172627_name=extractors-msc\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_capability_system_jdk_JDK=/home/bamboo/jdk1.8.0_66\nbamboo_capability_system_software_mongo=/usr/bin/mongo\nbamboo_plan_storageTag=plan-126976035\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_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-msc.git\nbamboo_repository_127172627_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.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-MSC-JOB1\nbamboo_planKey=CATS-MSC\nbamboo_planRepository_1_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git\nbamboo_planRepository_username=\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_repository_127172627_previous_revision_number=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_planRepository_1_branchName=master\n
build	18-Apr-2018 17:18:49	Sending build context to Docker daemon  2.284MB
build	18-Apr-2018 17:18:49	
build	18-Apr-2018 17:18:49	Step 1/11 : FROM clowder/pyclowder:1
build	18-Apr-2018 17:18:49	 ---> d1a9e970ed30
build	18-Apr-2018 17:18:49	Step 2/11 : MAINTAINER Rob Kooper <kooper@illinois.edu>
build	18-Apr-2018 17:18:49	 ---> Running in 1bbf4531c8c0
build	18-Apr-2018 17:18:50	Removing intermediate container 1bbf4531c8c0
build	18-Apr-2018 17:18:50	 ---> 199b32438235
build	18-Apr-2018 17:18:50	Step 3/11 : VOLUME /matlab
build	18-Apr-2018 17:18:50	 ---> Running in 4ec2d6840886
build	18-Apr-2018 17:18:50	Removing intermediate container 4ec2d6840886
build	18-Apr-2018 17:18:50	 ---> 7fada06ede8a
build	18-Apr-2018 17:18:50	Step 4/11 : ENV RABBITMQ_URI=""     RABBITMQ_EXCHANGE="clowder"     RABBITMQ_VHOST="%2F"     RABBITMQ_QUEUE="ncsa.msc.diagnosis"     MATLAB_BINARY="/matlab/bin/matlab"     MAIN_SCRIPT="diagnosis.py"
build	18-Apr-2018 17:18:51	 ---> Running in 60c3cacd1aeb
build	18-Apr-2018 17:18:51	Removing intermediate container 60c3cacd1aeb
build	18-Apr-2018 17:18:51	 ---> 16acceb9cc21
build	18-Apr-2018 17:18:51	Step 5/11 : USER root
build	18-Apr-2018 17:18:52	 ---> Running in 62acfac58e7d
build	18-Apr-2018 17:18:52	Removing intermediate container 62acfac58e7d
build	18-Apr-2018 17:18:52	 ---> b37ef4634ddb
build	18-Apr-2018 17:18:52	Step 6/11 : RUN pip install --upgrade pip
build	18-Apr-2018 17:18:53	 ---> Running in d355872bac14
build	18-Apr-2018 17:18:55	Collecting pip
build	18-Apr-2018 17:18:55	  Downloading https://files.pythonhosted.org/packages/62/a1/0d452b6901b0157a0134fd27ba89bf95a857fbda64ba52e1ca2cf61d8412/pip-10.0.0-py2.py3-none-any.whl (1.3MB)
build	18-Apr-2018 17:18:55	Installing collected packages: pip
build	18-Apr-2018 17:18:55	  Found existing installation: pip 8.1.1
build	18-Apr-2018 17:18:55	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	18-Apr-2018 17:18:56	Successfully installed pip-10.0.0
build	18-Apr-2018 17:18:58	Removing intermediate container d355872bac14
build	18-Apr-2018 17:18:58	 ---> 7821086222d9
build	18-Apr-2018 17:18:58	Step 7/11 : RUN apt-get -qq -y update && apt-get -y install         libxext6         libxmu6         libxt6         wget     && mkdir -p /matlab     && rm -rf /var/lib/apt/lists/*
build	18-Apr-2018 17:18:58	 ---> Running in 5689f2d41b92
build	18-Apr-2018 17:19:04	Reading package lists...
build	18-Apr-2018 17:19:04	Building dependency tree...
build	18-Apr-2018 17:19:04	Reading state information...
build	18-Apr-2018 17:19:04	The following additional packages will be installed:
build	18-Apr-2018 17:19:04	  libice6 libidn11 libsm6 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
build	18-Apr-2018 17:19:04	  x11-common
build	18-Apr-2018 17:19:04	The following NEW packages will be installed:
build	18-Apr-2018 17:19:04	  libice6 libidn11 libsm6 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
build	18-Apr-2018 17:19:04	  libxext6 libxmu6 libxt6 wget x11-common
build	18-Apr-2018 17:19:05	0 upgraded, 13 newly installed, 0 to remove and 43 not upgraded.
build	18-Apr-2018 17:19:05	Need to get 1402 kB of archives.
build	18-Apr-2018 17:19:05	After this operation, 5596 kB of additional disk space will be used.
build	18-Apr-2018 17:19:05	Get:1 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B]
build	18-Apr-2018 17:19:05	Get:2 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [11.0 kB]
build	18-Apr-2018 17:19:05	Get:3 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxcb1 amd64 1.11.1-1ubuntu1 [40.0 kB]
build	18-Apr-2018 17:19:05	Get:4 http://archive.ubuntu.com/ubuntu xenial/main amd64 libx11-data all 2:1.6.3-1ubuntu2 [113 kB]
build	18-Apr-2018 17:19:05	Get:5 http://archive.ubuntu.com/ubuntu xenial/main amd64 libx11-6 amd64 2:1.6.3-1ubuntu2 [571 kB]
build	18-Apr-2018 17:19:05	Get:6 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB]
build	18-Apr-2018 17:19:05	Get:7 http://archive.ubuntu.com/ubuntu xenial/main amd64 x11-common all 1:7.7+13ubuntu3 [22.4 kB]
build	18-Apr-2018 17:19:05	Get:8 http://archive.ubuntu.com/ubuntu xenial/main amd64 libice6 amd64 2:1.0.9-1 [39.2 kB]
build	18-Apr-2018 17:19:05	Get:9 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB]
build	18-Apr-2018 17:19:05	Get:10 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libidn11 amd64 1.32-3ubuntu1.2 [46.5 kB]
build	18-Apr-2018 17:19:05	Get:11 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 wget amd64 1.17.1-1ubuntu1.3 [299 kB]
build	18-Apr-2018 17:19:05	Get:12 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxt6 amd64 1:1.1.5-0ubuntu1 [160 kB]
build	18-Apr-2018 17:19:05	Get:13 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxmu6 amd64 2:1.1.2-2 [46.0 kB]
build	18-Apr-2018 17:19:06	debconf: delaying package configuration, since apt-utils is not installed
build	18-Apr-2018 17:19:06	Fetched 1402 kB in 0s (1515 kB/s)
build	18-Apr-2018 17:19:06	Selecting previously unselected package libxau6:amd64.
build	18-Apr-2018 17:19:06	(Reading database ... 
build	18-Apr-2018 17:19:06	(Reading database ... 5%
build	18-Apr-2018 17:19:06	(Reading database ... 10%
build	18-Apr-2018 17:19:06	(Reading database ... 15%
build	18-Apr-2018 17:19:06	(Reading database ... 20%
build	18-Apr-2018 17:19:06	(Reading database ... 25%
build	18-Apr-2018 17:19:06	(Reading database ... 30%
build	18-Apr-2018 17:19:06	(Reading database ... 35%
build	18-Apr-2018 17:19:06	(Reading database ... 40%
build	18-Apr-2018 17:19:06	(Reading database ... 45%
build	18-Apr-2018 17:19:06	(Reading database ... 50%
build	18-Apr-2018 17:19:06	(Reading database ... 55%
build	18-Apr-2018 17:19:06	(Reading database ... 60%
build	18-Apr-2018 17:19:06	(Reading database ... 65%
build	18-Apr-2018 17:19:06	(Reading database ... 70%
build	18-Apr-2018 17:19:06	(Reading database ... 75%
build	18-Apr-2018 17:19:06	(Reading database ... 80%
build	18-Apr-2018 17:19:06	(Reading database ... 85%
build	18-Apr-2018 17:19:06	(Reading database ... 90%
build	18-Apr-2018 17:19:06	(Reading database ... 95%
build	18-Apr-2018 17:19:06	(Reading database ... 100%
build	18-Apr-2018 17:19:06	(Reading database ... 6101 files and directories currently installed.)
build	18-Apr-2018 17:19:06	Preparing to unpack .../libxau6_1%3a1.0.8-1_amd64.deb ...
build	18-Apr-2018 17:19:06	Unpacking libxau6:amd64 (1:1.0.8-1) ...
build	18-Apr-2018 17:19:07	Selecting previously unselected package libxdmcp6:amd64.
build	18-Apr-2018 17:19:07	Preparing to unpack .../libxdmcp6_1%3a1.1.2-1.1_amd64.deb ...
build	18-Apr-2018 17:19:07	Unpacking libxdmcp6:amd64 (1:1.1.2-1.1) ...
build	18-Apr-2018 17:19:08	Selecting previously unselected package libxcb1:amd64.
build	18-Apr-2018 17:19:08	Preparing to unpack .../libxcb1_1.11.1-1ubuntu1_amd64.deb ...
build	18-Apr-2018 17:19:08	Unpacking libxcb1:amd64 (1.11.1-1ubuntu1) ...
build	18-Apr-2018 17:19:08	Selecting previously unselected package libx11-data.
build	18-Apr-2018 17:19:08	Preparing to unpack .../libx11-data_2%3a1.6.3-1ubuntu2_all.deb ...
build	18-Apr-2018 17:19:08	Unpacking libx11-data (2:1.6.3-1ubuntu2) ...
build	18-Apr-2018 17:19:09	Selecting previously unselected package libx11-6:amd64.
build	18-Apr-2018 17:19:09	Preparing to unpack .../libx11-6_2%3a1.6.3-1ubuntu2_amd64.deb ...
build	18-Apr-2018 17:19:09	Unpacking libx11-6:amd64 (2:1.6.3-1ubuntu2) ...
build	18-Apr-2018 17:19:10	Selecting previously unselected package libxext6:amd64.
build	18-Apr-2018 17:19:10	Preparing to unpack .../libxext6_2%3a1.3.3-1_amd64.deb ...
build	18-Apr-2018 17:19:10	Unpacking libxext6:amd64 (2:1.3.3-1) ...
build	18-Apr-2018 17:19:11	Selecting previously unselected package x11-common.
build	18-Apr-2018 17:19:11	Preparing to unpack .../x11-common_1%3a7.7+13ubuntu3_all.deb ...
build	18-Apr-2018 17:19:11	Unpacking x11-common (1:7.7+13ubuntu3) ...
build	18-Apr-2018 17:19:12	Selecting previously unselected package libice6:amd64.
build	18-Apr-2018 17:19:12	Preparing to unpack .../libice6_2%3a1.0.9-1_amd64.deb ...
build	18-Apr-2018 17:19:12	Unpacking libice6:amd64 (2:1.0.9-1) ...
build	18-Apr-2018 17:19:14	Selecting previously unselected package libsm6:amd64.
build	18-Apr-2018 17:19:14	Preparing to unpack .../libsm6_2%3a1.2.2-1_amd64.deb ...
build	18-Apr-2018 17:19:14	Unpacking libsm6:amd64 (2:1.2.2-1) ...
build	18-Apr-2018 17:19:15	Selecting previously unselected package libidn11:amd64.
build	18-Apr-2018 17:19:15	Preparing to unpack .../libidn11_1.32-3ubuntu1.2_amd64.deb ...
build	18-Apr-2018 17:19:15	Unpacking libidn11:amd64 (1.32-3ubuntu1.2) ...
build	18-Apr-2018 17:19:16	Selecting previously unselected package wget.
build	18-Apr-2018 17:19:16	Preparing to unpack .../wget_1.17.1-1ubuntu1.3_amd64.deb ...
build	18-Apr-2018 17:19:16	Unpacking wget (1.17.1-1ubuntu1.3) ...
build	18-Apr-2018 17:19:17	Selecting previously unselected package libxt6:amd64.
build	18-Apr-2018 17:19:17	Preparing to unpack .../libxt6_1%3a1.1.5-0ubuntu1_amd64.deb ...
build	18-Apr-2018 17:19:17	Unpacking libxt6:amd64 (1:1.1.5-0ubuntu1) ...
build	18-Apr-2018 17:19:18	Selecting previously unselected package libxmu6:amd64.
build	18-Apr-2018 17:19:18	Preparing to unpack .../libxmu6_2%3a1.1.2-2_amd64.deb ...
build	18-Apr-2018 17:19:18	Unpacking libxmu6:amd64 (2:1.1.2-2) ...
build	18-Apr-2018 17:19:18	Processing triggers for libc-bin (2.23-0ubuntu9) ...
build	18-Apr-2018 17:19:18	Processing triggers for systemd (229-4ubuntu19) ...
build	18-Apr-2018 17:19:19	Setting up libxau6:amd64 (1:1.0.8-1) ...
build	18-Apr-2018 17:19:19	Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ...
build	18-Apr-2018 17:19:19	Setting up libxcb1:amd64 (1.11.1-1ubuntu1) ...
build	18-Apr-2018 17:19:20	Setting up libx11-data (2:1.6.3-1ubuntu2) ...
build	18-Apr-2018 17:19:20	Setting up libx11-6:amd64 (2:1.6.3-1ubuntu2) ...
build	18-Apr-2018 17:19:20	Setting up libxext6:amd64 (2:1.3.3-1) ...
build	18-Apr-2018 17:19:21	Setting up x11-common (1:7.7+13ubuntu3) ...
build	18-Apr-2018 17:19:23	debconf: unable to initialize frontend: Dialog
build	18-Apr-2018 17:19:23	debconf: (TERM is not set, so the dialog frontend is not usable.)
build	18-Apr-2018 17:19:23	debconf: falling back to frontend: Readline
build	18-Apr-2018 17:19:23	debconf: unable to initialize frontend: Readline
build	18-Apr-2018 17:19:23	debconf: (Can't locate Term/ReadLine.pm in @INC (you may need to install the Term::ReadLine module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /usr/share/perl5/Debconf/FrontEnd/Readline.pm line 7.)
build	18-Apr-2018 17:19:23	debconf: falling back to frontend: Teletype
build	18-Apr-2018 17:19:23	update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
build	18-Apr-2018 17:19:23	invoke-rc.d: could not determine current runlevel
build	18-Apr-2018 17:19:23	invoke-rc.d: policy-rc.d denied execution of start.
build	18-Apr-2018 17:19:23	Setting up libice6:amd64 (2:1.0.9-1) ...
build	18-Apr-2018 17:19:23	Setting up libsm6:amd64 (2:1.2.2-1) ...
build	18-Apr-2018 17:19:24	Setting up libidn11:amd64 (1.32-3ubuntu1.2) ...
build	18-Apr-2018 17:19:24	Setting up wget (1.17.1-1ubuntu1.3) ...
build	18-Apr-2018 17:19:24	Setting up libxt6:amd64 (1:1.1.5-0ubuntu1) ...
build	18-Apr-2018 17:19:25	Setting up libxmu6:amd64 (2:1.1.2-2) ...
build	18-Apr-2018 17:19:25	Processing triggers for libc-bin (2.23-0ubuntu9) ...
build	18-Apr-2018 17:19:25	Processing triggers for systemd (229-4ubuntu19) ...
build	18-Apr-2018 17:19:27	Removing intermediate container 5689f2d41b92
build	18-Apr-2018 17:19:27	 ---> 3b85732d8c98
build	18-Apr-2018 17:19:27	Step 8/11 : USER clowder
build	18-Apr-2018 17:19:28	 ---> Running in 82387c13df1a
build	18-Apr-2018 17:19:28	Removing intermediate container 82387c13df1a
build	18-Apr-2018 17:19:28	 ---> d80b9bd311d3
build	18-Apr-2018 17:19:28	Step 9/11 : COPY entrypoint.sh *.py *.m data/*.mat *.json /home/clowder/
build	18-Apr-2018 17:19:30	 ---> 8b415eba15fc
build	18-Apr-2018 17:19:30	Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"]
build	18-Apr-2018 17:19:30	 ---> Running in 73400d9700ae
build	18-Apr-2018 17:19:31	Removing intermediate container 73400d9700ae
build	18-Apr-2018 17:19:31	 ---> 492d3d285daa
build	18-Apr-2018 17:19:31	Step 11/11 : CMD ["extractor"]
build	18-Apr-2018 17:19:31	 ---> Running in 54d593711e34
build	18-Apr-2018 17:19:32	Removing intermediate container 54d593711e34
build	18-Apr-2018 17:19:32	 ---> 48c1c411b9b7
build	18-Apr-2018 17:19:32	Successfully built 48c1c411b9b7
build	18-Apr-2018 17:19:32	Successfully tagged 17576:latest
build	18-Apr-2018 17:19:32	The push refers to repository [docker.io/clowder/extractors-msc-kidney]
build	18-Apr-2018 17:19:32	a2ffe2e4f347: Preparing
build	18-Apr-2018 17:19:32	41c6ef0756f7: Preparing
build	18-Apr-2018 17:19:32	80d567800b34: Preparing
build	18-Apr-2018 17:19:32	0cdb02ac1d86: Preparing
build	18-Apr-2018 17:19:32	f2297bdfc824: Preparing
build	18-Apr-2018 17:19:32	0fbe2bcb1bf9: Preparing
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build	18-Apr-2018 17:19:32	7f7a065d245a: Preparing
build	18-Apr-2018 17:19:32	f96e6b25195f: Preparing
build	18-Apr-2018 17:19:32	c56153825175: Preparing
build	18-Apr-2018 17:19:32	ae620432889d: Preparing
build	18-Apr-2018 17:19:32	a2022691bf95: Preparing
build	18-Apr-2018 17:19:32	59669fcdd5eb: Waiting
build	18-Apr-2018 17:19:32	7f7a065d245a: Waiting
build	18-Apr-2018 17:19:32	f96e6b25195f: Waiting
build	18-Apr-2018 17:19:32	c56153825175: Waiting
build	18-Apr-2018 17:19:32	ae620432889d: Waiting
build	18-Apr-2018 17:19:32	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:19:32	a2022691bf95: Waiting
build	18-Apr-2018 17:19:33	0cdb02ac1d86: Layer already exists
build	18-Apr-2018 17:19:33	f2297bdfc824: Layer already exists
build	18-Apr-2018 17:19:33	0fbe2bcb1bf9: Layer already exists
build	18-Apr-2018 17:19:33	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:19:33	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:19:33	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:19:33	c56153825175: Layer already exists
build	18-Apr-2018 17:19:33	ae620432889d: Layer already exists
build	18-Apr-2018 17:19:33	a2022691bf95: Layer already exists
build	18-Apr-2018 17:19:34	a2ffe2e4f347: Pushed
build	18-Apr-2018 17:19:34	41c6ef0756f7: Pushed
build	18-Apr-2018 17:19:34	80d567800b34: Pushed
build	18-Apr-2018 17:19:37	browndog_v0.2.0: digest: sha256:6b03848eec43baa01d47e32c994b064d9ea0cc3b081dfce35dc2cd1053da45e2 size: 2826
build	18-Apr-2018 17:19:37	The push refers to repository [docker.io/clowder/extractors-msc-kidney]
build	18-Apr-2018 17:19:37	a2ffe2e4f347: Preparing
build	18-Apr-2018 17:19:37	41c6ef0756f7: Preparing
build	18-Apr-2018 17:19:37	80d567800b34: Preparing
build	18-Apr-2018 17:19:37	0cdb02ac1d86: Preparing
build	18-Apr-2018 17:19:37	f2297bdfc824: Preparing
build	18-Apr-2018 17:19:37	0fbe2bcb1bf9: Preparing
build	18-Apr-2018 17:19:37	59669fcdd5eb: Preparing
build	18-Apr-2018 17:19:37	7f7a065d245a: Preparing
build	18-Apr-2018 17:19:37	f96e6b25195f: Preparing
build	18-Apr-2018 17:19:37	c56153825175: Preparing
build	18-Apr-2018 17:19:37	ae620432889d: Preparing
build	18-Apr-2018 17:19:37	a2022691bf95: Preparing
build	18-Apr-2018 17:19:37	f96e6b25195f: Waiting
build	18-Apr-2018 17:19:37	ae620432889d: Waiting
build	18-Apr-2018 17:19:37	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:19:37	c56153825175: Waiting
build	18-Apr-2018 17:19:37	59669fcdd5eb: Waiting
build	18-Apr-2018 17:19:37	a2022691bf95: Waiting
build	18-Apr-2018 17:19:37	7f7a065d245a: Waiting
build	18-Apr-2018 17:19:38	80d567800b34: Layer already exists
build	18-Apr-2018 17:19:38	f2297bdfc824: Layer already exists
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build	18-Apr-2018 17:19:38	0cdb02ac1d86: Layer already exists
build	18-Apr-2018 17:19:38	a2ffe2e4f347: Layer already exists
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build	18-Apr-2018 17:19:38	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:19:38	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:19:38	c56153825175: Layer already exists
build	18-Apr-2018 17:19:38	ae620432889d: Layer already exists
build	18-Apr-2018 17:19:38	a2022691bf95: Layer already exists
build	18-Apr-2018 17:19:38	browndog_v0.3.0: digest: sha256:6b03848eec43baa01d47e32c994b064d9ea0cc3b081dfce35dc2cd1053da45e2 size: 2826
build	18-Apr-2018 17:19:39	The push refers to repository [docker.io/clowder/extractors-msc-kidney]
build	18-Apr-2018 17:19:39	a2ffe2e4f347: Preparing
build	18-Apr-2018 17:19:39	41c6ef0756f7: Preparing
build	18-Apr-2018 17:19:39	80d567800b34: Preparing
build	18-Apr-2018 17:19:39	0cdb02ac1d86: Preparing
build	18-Apr-2018 17:19:39	f2297bdfc824: Preparing
build	18-Apr-2018 17:19:39	0fbe2bcb1bf9: Preparing
build	18-Apr-2018 17:19:39	59669fcdd5eb: Preparing
build	18-Apr-2018 17:19:39	7f7a065d245a: Preparing
build	18-Apr-2018 17:19:39	f96e6b25195f: Preparing
build	18-Apr-2018 17:19:39	c56153825175: Preparing
build	18-Apr-2018 17:19:39	ae620432889d: Preparing
build	18-Apr-2018 17:19:39	a2022691bf95: Preparing
build	18-Apr-2018 17:19:39	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:19:39	f96e6b25195f: Waiting
build	18-Apr-2018 17:19:39	c56153825175: Waiting
build	18-Apr-2018 17:19:39	59669fcdd5eb: Waiting
build	18-Apr-2018 17:19:39	ae620432889d: Waiting
build	18-Apr-2018 17:19:39	a2022691bf95: Waiting
build	18-Apr-2018 17:19:39	a2ffe2e4f347: Layer already exists
build	18-Apr-2018 17:19:39	0cdb02ac1d86: Layer already exists
build	18-Apr-2018 17:19:39	41c6ef0756f7: Layer already exists
build	18-Apr-2018 17:19:39	80d567800b34: Layer already exists
build	18-Apr-2018 17:19:39	f2297bdfc824: Layer already exists
build	18-Apr-2018 17:19:39	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:19:39	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:19:39	c56153825175: Layer already exists
build	18-Apr-2018 17:19:39	0fbe2bcb1bf9: Layer already exists
build	18-Apr-2018 17:19:39	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:19:39	ae620432889d: Layer already exists
build	18-Apr-2018 17:19:40	a2022691bf95: Layer already exists
build	18-Apr-2018 17:19:40	latest: digest: sha256:6b03848eec43baa01d47e32c994b064d9ea0cc3b081dfce35dc2cd1053da45e2 size: 2826
build	18-Apr-2018 17:19:40	Untagged: 17576:latest
build	18-Apr-2018 17:19:40	Sending build context to Docker daemon  67.07kB
build	18-Apr-2018 17:19:40	
build	18-Apr-2018 17:19:40	Step 1/11 : FROM clowder/pyclowder:1
build	18-Apr-2018 17:19:40	 ---> d1a9e970ed30
build	18-Apr-2018 17:19:40	Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu>
build	18-Apr-2018 17:19:40	 ---> Running in 79d7ff2098a5
build	18-Apr-2018 17:19:41	Removing intermediate container 79d7ff2098a5
build	18-Apr-2018 17:19:41	 ---> 46bf81116550
build	18-Apr-2018 17:19:41	Step 3/11 : ENV RABBITMQ_URI=""     RABBITMQ_EXCHANGE="clowder"     RABBITMQ_VHOST="%2F"     RABBITMQ_QUEUE="ncsa.msc.IsletExtractor"     MONGO_URI=""    DB_USERNAME=""    DB_PASSWORD=""    MAIN_SCRIPT="extractor-Islet.py"
build	18-Apr-2018 17:19:41	 ---> Running in 70d108ad9a77
build	18-Apr-2018 17:19:41	Removing intermediate container 70d108ad9a77
build	18-Apr-2018 17:19:41	 ---> dd2ad7a1b589
build	18-Apr-2018 17:19:41	Step 4/11 : USER root
build	18-Apr-2018 17:19:42	 ---> Running in 9d27546844b4
build	18-Apr-2018 17:19:42	Removing intermediate container 9d27546844b4
build	18-Apr-2018 17:19:42	 ---> 91c3848d3f31
build	18-Apr-2018 17:19:42	Step 5/11 : COPY requirements.txt /home/clowder/
build	18-Apr-2018 17:19:43	 ---> c75c51142d7c
build	18-Apr-2018 17:19:43	Step 6/11 : RUN pip install --upgrade pip
build	18-Apr-2018 17:19:43	 ---> Running in f69a3194a099
build	18-Apr-2018 17:19:45	Collecting pip
build	18-Apr-2018 17:19:45	  Downloading https://files.pythonhosted.org/packages/62/a1/0d452b6901b0157a0134fd27ba89bf95a857fbda64ba52e1ca2cf61d8412/pip-10.0.0-py2.py3-none-any.whl (1.3MB)
build	18-Apr-2018 17:19:45	Installing collected packages: pip
build	18-Apr-2018 17:19:45	  Found existing installation: pip 8.1.1
build	18-Apr-2018 17:19:45	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	18-Apr-2018 17:19:46	Successfully installed pip-10.0.0
build	18-Apr-2018 17:19:47	Removing intermediate container f69a3194a099
build	18-Apr-2018 17:19:47	 ---> 1c0d3f87f103
build	18-Apr-2018 17:19:47	Step 7/11 : RUN pip install -r /home/clowder/requirements.txt
build	18-Apr-2018 17:19:48	 ---> Running in 237c06055c8d
build	18-Apr-2018 17:19:48	Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) (1.2.1)
build	18-Apr-2018 17:19:48	Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2))
build	18-Apr-2018 17:19:49	  Downloading https://files.pythonhosted.org/packages/96/53/3782b6cc03500c0949a7ba9dba0c70da95d63d0ed4a04446123987ff983f/openpyxl-1.6.2.tar.gz (199kB)
build	18-Apr-2018 17:19:49	Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3))
build	18-Apr-2018 17:19:49	  Downloading https://files.pythonhosted.org/packages/2b/5b/4c5b6eafc63e0985b926267579a1e2534af70df0a45932f0c23fcc5f1b88/pika-0.9.14.tar.gz (72kB)
build	18-Apr-2018 17:19:49	Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4))
build	18-Apr-2018 17:19:50	  Downloading https://files.pythonhosted.org/packages/d7/94/9aa9ddd3e885caa307c0db8af5a1f5d266d3db44e1ae89bd4e14841ab8d0/pymongo-3.2.1.tar.gz (647kB)
build	18-Apr-2018 17:19:51	Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5))
build	18-Apr-2018 17:19:51	  Downloading https://files.pythonhosted.org/packages/e2/8d/af599c0388f46775c6b039d8b9c4acda2f6ef86787312a35291fff4cb7ca/pytz-2014.3.tar.bz2 (158kB)
build	18-Apr-2018 17:19:52	Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6))
build	18-Apr-2018 17:19:52	  Downloading https://files.pythonhosted.org/packages/7d/15/6efffc6aee666e1456852c2bf1d483b46bf971a2d509b35a98fc3eae1c60/requests-2.2.1-py2.py3-none-any.whl (625kB)
build	18-Apr-2018 17:19:52	Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) (0.1.2)
build	18-Apr-2018 17:19:52	Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8))
build	18-Apr-2018 17:19:52	  Downloading https://files.pythonhosted.org/packages/b1/13/6fbcb55fef0b34c70cb3753741eaafc0e91553a1318653587a7d145caf15/xlrd-0.9.3.tar.gz (178kB)
build	18-Apr-2018 17:19:52	Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd
build	18-Apr-2018 17:19:52	  Running setup.py install for openpyxl: started
build	18-Apr-2018 17:19:52	    Running setup.py install for openpyxl: finished with status 'done'
build	18-Apr-2018 17:19:52	  Found existing installation: pika 0.11.0
build	18-Apr-2018 17:19:52	    Uninstalling pika-0.11.0:
build	18-Apr-2018 17:19:55	      Successfully uninstalled pika-0.11.0
build	18-Apr-2018 17:19:55	  Running setup.py install for pika: started
build	18-Apr-2018 17:19:55	    Running setup.py install for pika: finished with status 'done'
build	18-Apr-2018 17:19:55	  Running setup.py install for pymongo: started
build	18-Apr-2018 17:19:55	    Running setup.py install for pymongo: finished with status 'done'
build	18-Apr-2018 17:19:55	  Running setup.py install for pytz: started
build	18-Apr-2018 17:19:56	    Running setup.py install for pytz: finished with status 'done'
build	18-Apr-2018 17:19:56	  Found existing installation: requests 2.18.4
build	18-Apr-2018 17:19:56	    Uninstalling requests-2.18.4:
build	18-Apr-2018 17:19:58	      Successfully uninstalled requests-2.18.4
build	18-Apr-2018 17:19:58	  Running setup.py install for xlrd: started
build	18-Apr-2018 17:19:59	    Running setup.py install for xlrd: finished with status 'done'
build	18-Apr-2018 17:19:59	Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3
build	18-Apr-2018 17:20:00	Removing intermediate container 237c06055c8d
build	18-Apr-2018 17:20:00	 ---> cf2cf73f0483
build	18-Apr-2018 17:20:00	Step 8/11 : USER clowder
build	18-Apr-2018 17:20:01	 ---> Running in 28dbbc47bc00
build	18-Apr-2018 17:20:01	Removing intermediate container 28dbbc47bc00
build	18-Apr-2018 17:20:01	 ---> f3a8548c2226
build	18-Apr-2018 17:20:01	Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/
build	18-Apr-2018 17:20:02	 ---> bf7cda114213
build	18-Apr-2018 17:20:02	Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"]
build	18-Apr-2018 17:20:02	 ---> Running in 6eeab2104213
build	18-Apr-2018 17:20:03	Removing intermediate container 6eeab2104213
build	18-Apr-2018 17:20:03	 ---> 11ec3b401994
build	18-Apr-2018 17:20:03	Step 11/11 : CMD ["extractor"]
build	18-Apr-2018 17:20:03	 ---> Running in eaf3c3051f0e
build	18-Apr-2018 17:20:03	Removing intermediate container eaf3c3051f0e
build	18-Apr-2018 17:20:03	 ---> e6e961517398
build	18-Apr-2018 17:20:03	Successfully built e6e961517398
build	18-Apr-2018 17:20:03	Successfully tagged 17576:latest
build	18-Apr-2018 17:20:04	The push refers to repository [docker.io/clowder/extractors-msc-islet]
build	18-Apr-2018 17:20:04	82cd06ddb546: Preparing
build	18-Apr-2018 17:20:04	72da6a0b7931: Preparing
build	18-Apr-2018 17:20:04	cd077f8b5a6d: Preparing
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build	18-Apr-2018 17:20:04	ae620432889d: Preparing
build	18-Apr-2018 17:20:04	a2022691bf95: Preparing
build	18-Apr-2018 17:20:04	f2297bdfc824: Waiting
build	18-Apr-2018 17:20:04	f96e6b25195f: Waiting
build	18-Apr-2018 17:20:04	c56153825175: Waiting
build	18-Apr-2018 17:20:04	0fbe2bcb1bf9: Waiting
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build	18-Apr-2018 17:20:04	ae620432889d: Waiting
build	18-Apr-2018 17:20:04	7f7a065d245a: Waiting
build	18-Apr-2018 17:20:04	a2022691bf95: Waiting
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build	18-Apr-2018 17:20:05	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:20:05	82cd06ddb546: Pushed
build	18-Apr-2018 17:20:05	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:20:05	273abc9933de: Pushed
build	18-Apr-2018 17:20:05	c56153825175: Layer already exists
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build	18-Apr-2018 17:20:06	ae620432889d: Layer already exists
build	18-Apr-2018 17:20:06	a2022691bf95: Layer already exists
build	18-Apr-2018 17:20:06	cd077f8b5a6d: Pushed
build	18-Apr-2018 17:20:06	72da6a0b7931: Pushed
build	18-Apr-2018 17:20:08	browndog_v0.2.0: digest: sha256:5da9646126fd0ebca15b3a4131f98734229fb7e1a42207650f836ae2dd43ca38 size: 3031
build	18-Apr-2018 17:20:08	The push refers to repository [docker.io/clowder/extractors-msc-islet]
build	18-Apr-2018 17:20:08	82cd06ddb546: Preparing
build	18-Apr-2018 17:20:08	72da6a0b7931: Preparing
build	18-Apr-2018 17:20:08	cd077f8b5a6d: Preparing
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build	18-Apr-2018 17:20:08	59669fcdd5eb: Preparing
build	18-Apr-2018 17:20:08	7f7a065d245a: Preparing
build	18-Apr-2018 17:20:08	f96e6b25195f: Preparing
build	18-Apr-2018 17:20:08	c56153825175: Preparing
build	18-Apr-2018 17:20:08	ae620432889d: Preparing
build	18-Apr-2018 17:20:08	a2022691bf95: Preparing
build	18-Apr-2018 17:20:08	f2297bdfc824: Waiting
build	18-Apr-2018 17:20:08	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:20:08	59669fcdd5eb: Waiting
build	18-Apr-2018 17:20:08	7f7a065d245a: Waiting
build	18-Apr-2018 17:20:08	f96e6b25195f: Waiting
build	18-Apr-2018 17:20:08	c56153825175: Waiting
build	18-Apr-2018 17:20:08	ae620432889d: Waiting
build	18-Apr-2018 17:20:08	a2022691bf95: Waiting
build	18-Apr-2018 17:20:09	82cd06ddb546: Layer already exists
build	18-Apr-2018 17:20:09	273abc9933de: Layer already exists
build	18-Apr-2018 17:20:09	0cdb02ac1d86: Layer already exists
build	18-Apr-2018 17:20:09	cd077f8b5a6d: Layer already exists
build	18-Apr-2018 17:20:09	0fbe2bcb1bf9: Layer already exists
build	18-Apr-2018 17:20:09	72da6a0b7931: Layer already exists
build	18-Apr-2018 17:20:09	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:20:09	f2297bdfc824: Layer already exists
build	18-Apr-2018 17:20:09	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:20:09	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:20:09	c56153825175: Layer already exists
build	18-Apr-2018 17:20:09	ae620432889d: Layer already exists
build	18-Apr-2018 17:20:09	a2022691bf95: Layer already exists
build	18-Apr-2018 17:20:09	browndog_v0.3.0: digest: sha256:5da9646126fd0ebca15b3a4131f98734229fb7e1a42207650f836ae2dd43ca38 size: 3031
build	18-Apr-2018 17:20:10	The push refers to repository [docker.io/clowder/extractors-msc-islet]
build	18-Apr-2018 17:20:10	82cd06ddb546: Preparing
build	18-Apr-2018 17:20:10	72da6a0b7931: Preparing
build	18-Apr-2018 17:20:10	cd077f8b5a6d: Preparing
build	18-Apr-2018 17:20:10	273abc9933de: Preparing
build	18-Apr-2018 17:20:10	0cdb02ac1d86: Preparing
build	18-Apr-2018 17:20:10	f2297bdfc824: Preparing
build	18-Apr-2018 17:20:10	0fbe2bcb1bf9: Preparing
build	18-Apr-2018 17:20:10	59669fcdd5eb: Preparing
build	18-Apr-2018 17:20:10	7f7a065d245a: Preparing
build	18-Apr-2018 17:20:10	f96e6b25195f: Preparing
build	18-Apr-2018 17:20:10	c56153825175: Preparing
build	18-Apr-2018 17:20:10	ae620432889d: Preparing
build	18-Apr-2018 17:20:10	a2022691bf95: Preparing
build	18-Apr-2018 17:20:10	f2297bdfc824: Waiting
build	18-Apr-2018 17:20:10	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:20:10	59669fcdd5eb: Waiting
build	18-Apr-2018 17:20:10	7f7a065d245a: Waiting
build	18-Apr-2018 17:20:10	f96e6b25195f: Waiting
build	18-Apr-2018 17:20:10	c56153825175: Waiting
build	18-Apr-2018 17:20:10	ae620432889d: Waiting
build	18-Apr-2018 17:20:10	a2022691bf95: Waiting
build	18-Apr-2018 17:20:10	0cdb02ac1d86: Layer already exists
build	18-Apr-2018 17:20:10	273abc9933de: Layer already exists
build	18-Apr-2018 17:20:10	72da6a0b7931: Layer already exists
build	18-Apr-2018 17:20:10	82cd06ddb546: Layer already exists
build	18-Apr-2018 17:20:10	cd077f8b5a6d: Layer already exists
build	18-Apr-2018 17:20:10	f2297bdfc824: Layer already exists
build	18-Apr-2018 17:20:10	0fbe2bcb1bf9: Layer already exists
build	18-Apr-2018 17:20:10	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:20:10	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:20:11	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:20:11	a2022691bf95: Layer already exists
build	18-Apr-2018 17:20:11	c56153825175: Layer already exists
build	18-Apr-2018 17:20:11	ae620432889d: Layer already exists
build	18-Apr-2018 17:20:11	latest: digest: sha256:5da9646126fd0ebca15b3a4131f98734229fb7e1a42207650f836ae2dd43ca38 size: 3031
build	18-Apr-2018 17:20:11	Untagged: 17576:latest
build	18-Apr-2018 17:20:11	Sending build context to Docker daemon  66.05kB
build	18-Apr-2018 17:20:11	
build	18-Apr-2018 17:20:11	Step 1/11 : FROM clowder/pyclowder:1
build	18-Apr-2018 17:20:11	 ---> d1a9e970ed30
build	18-Apr-2018 17:20:11	Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu>
build	18-Apr-2018 17:20:11	 ---> Using cache
build	18-Apr-2018 17:20:11	 ---> 46bf81116550
build	18-Apr-2018 17:20:11	Step 3/11 : ENV RABBITMQ_URI=""     RABBITMQ_EXCHANGE="clowder"     RABBITMQ_VHOST="%2F"     RABBITMQ_QUEUE="ncsa.msc.ChemCBCExtractor"     MONGO_URI=""    DB_USERNAME=""    DB_PASSWORD=""    MAIN_SCRIPT="extractor-Chem.py"
build	18-Apr-2018 17:20:11	 ---> Running in 6fd3d157c95a
build	18-Apr-2018 17:20:12	Removing intermediate container 6fd3d157c95a
build	18-Apr-2018 17:20:12	 ---> d4b5f9ca7750
build	18-Apr-2018 17:20:12	Step 4/11 : USER root
build	18-Apr-2018 17:20:12	 ---> Running in 29a7a3dbf225
build	18-Apr-2018 17:20:13	Removing intermediate container 29a7a3dbf225
build	18-Apr-2018 17:20:13	 ---> a99230797089
build	18-Apr-2018 17:20:13	Step 5/11 : COPY requirements.txt /home/clowder/
build	18-Apr-2018 17:20:13	 ---> 065a544b0599
build	18-Apr-2018 17:20:13	Step 6/11 : RUN pip install --upgrade pip
build	18-Apr-2018 17:20:13	 ---> Running in 0abedfe7f9f0
build	18-Apr-2018 17:20:15	Collecting pip
build	18-Apr-2018 17:20:15	  Downloading https://files.pythonhosted.org/packages/62/a1/0d452b6901b0157a0134fd27ba89bf95a857fbda64ba52e1ca2cf61d8412/pip-10.0.0-py2.py3-none-any.whl (1.3MB)
build	18-Apr-2018 17:20:15	Installing collected packages: pip
build	18-Apr-2018 17:20:15	  Found existing installation: pip 8.1.1
build	18-Apr-2018 17:20:15	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	18-Apr-2018 17:20:16	Successfully installed pip-10.0.0
build	18-Apr-2018 17:20:17	Removing intermediate container 0abedfe7f9f0
build	18-Apr-2018 17:20:17	 ---> df6d2e7d1130
build	18-Apr-2018 17:20:17	Step 7/11 : RUN pip install -r /home/clowder/requirements.txt
build	18-Apr-2018 17:20:18	 ---> Running in a6c38786dbd2
build	18-Apr-2018 17:20:18	Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) (1.2.1)
build	18-Apr-2018 17:20:18	Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2))
build	18-Apr-2018 17:20:18	  Downloading https://files.pythonhosted.org/packages/96/53/3782b6cc03500c0949a7ba9dba0c70da95d63d0ed4a04446123987ff983f/openpyxl-1.6.2.tar.gz (199kB)
build	18-Apr-2018 17:20:19	Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3))
build	18-Apr-2018 17:20:19	  Downloading https://files.pythonhosted.org/packages/2b/5b/4c5b6eafc63e0985b926267579a1e2534af70df0a45932f0c23fcc5f1b88/pika-0.9.14.tar.gz (72kB)
build	18-Apr-2018 17:20:19	Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4))
build	18-Apr-2018 17:20:20	  Downloading https://files.pythonhosted.org/packages/d7/94/9aa9ddd3e885caa307c0db8af5a1f5d266d3db44e1ae89bd4e14841ab8d0/pymongo-3.2.1.tar.gz (647kB)
build	18-Apr-2018 17:20:20	Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5))
build	18-Apr-2018 17:20:20	  Downloading https://files.pythonhosted.org/packages/e2/8d/af599c0388f46775c6b039d8b9c4acda2f6ef86787312a35291fff4cb7ca/pytz-2014.3.tar.bz2 (158kB)
build	18-Apr-2018 17:20:21	Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6))
build	18-Apr-2018 17:20:21	  Downloading https://files.pythonhosted.org/packages/7d/15/6efffc6aee666e1456852c2bf1d483b46bf971a2d509b35a98fc3eae1c60/requests-2.2.1-py2.py3-none-any.whl (625kB)
build	18-Apr-2018 17:20:21	Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) (0.1.2)
build	18-Apr-2018 17:20:21	Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8))
build	18-Apr-2018 17:20:21	  Downloading https://files.pythonhosted.org/packages/b1/13/6fbcb55fef0b34c70cb3753741eaafc0e91553a1318653587a7d145caf15/xlrd-0.9.3.tar.gz (178kB)
build	18-Apr-2018 17:20:21	Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd
build	18-Apr-2018 17:20:21	  Running setup.py install for openpyxl: started
build	18-Apr-2018 17:20:22	    Running setup.py install for openpyxl: finished with status 'done'
build	18-Apr-2018 17:20:22	  Found existing installation: pika 0.11.0
build	18-Apr-2018 17:20:22	    Uninstalling pika-0.11.0:
build	18-Apr-2018 17:20:25	      Successfully uninstalled pika-0.11.0
build	18-Apr-2018 17:20:25	  Running setup.py install for pika: started
build	18-Apr-2018 17:20:25	    Running setup.py install for pika: finished with status 'done'
build	18-Apr-2018 17:20:25	  Running setup.py install for pymongo: started
build	18-Apr-2018 17:20:25	    Running setup.py install for pymongo: finished with status 'done'
build	18-Apr-2018 17:20:25	  Running setup.py install for pytz: started
build	18-Apr-2018 17:20:26	    Running setup.py install for pytz: finished with status 'done'
build	18-Apr-2018 17:20:26	  Found existing installation: requests 2.18.4
build	18-Apr-2018 17:20:26	    Uninstalling requests-2.18.4:
build	18-Apr-2018 17:20:28	      Successfully uninstalled requests-2.18.4
build	18-Apr-2018 17:20:28	  Running setup.py install for xlrd: started
build	18-Apr-2018 17:20:29	    Running setup.py install for xlrd: finished with status 'done'
build	18-Apr-2018 17:20:29	Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3
build	18-Apr-2018 17:20:31	Removing intermediate container a6c38786dbd2
build	18-Apr-2018 17:20:31	 ---> 4de36593cd66
build	18-Apr-2018 17:20:31	Step 8/11 : USER clowder
build	18-Apr-2018 17:20:31	 ---> Running in 378ca44eb77f
build	18-Apr-2018 17:20:31	Removing intermediate container 378ca44eb77f
build	18-Apr-2018 17:20:31	 ---> 74b4d587dc9f
build	18-Apr-2018 17:20:31	Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/
build	18-Apr-2018 17:20:33	 ---> d386756a41cd
build	18-Apr-2018 17:20:33	Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"]
build	18-Apr-2018 17:20:33	 ---> Running in 342d333a6fdb
build	18-Apr-2018 17:20:34	Removing intermediate container 342d333a6fdb
build	18-Apr-2018 17:20:34	 ---> 452106dfbd0f
build	18-Apr-2018 17:20:34	Step 11/11 : CMD ["extractor"]
build	18-Apr-2018 17:20:34	 ---> Running in 86d0cd823fba
build	18-Apr-2018 17:20:34	Removing intermediate container 86d0cd823fba
build	18-Apr-2018 17:20:34	 ---> 1f0d0a7da8dd
build	18-Apr-2018 17:20:34	Successfully built 1f0d0a7da8dd
build	18-Apr-2018 17:20:34	Successfully tagged 17576:latest
build	18-Apr-2018 17:20:35	The push refers to repository [docker.io/clowder/extractors-msc-chemcbc]
build	18-Apr-2018 17:20:35	9ffdd3dc6673: Preparing
build	18-Apr-2018 17:20:35	695eaee0b84c: Preparing
build	18-Apr-2018 17:20:35	4685a92e073c: Preparing
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build	18-Apr-2018 17:20:35	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:20:35	59669fcdd5eb: Waiting
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build	18-Apr-2018 17:20:35	ae620432889d: Waiting
build	18-Apr-2018 17:20:35	a2022691bf95: Waiting
build	18-Apr-2018 17:20:35	f2297bdfc824: Waiting
build	18-Apr-2018 17:20:35	0cdb02ac1d86: Layer already exists
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build	18-Apr-2018 17:20:36	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:20:36	1cd7cbd2febc: Pushed
build	18-Apr-2018 17:20:36	9ffdd3dc6673: Pushed
build	18-Apr-2018 17:20:36	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:20:36	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:20:36	c56153825175: Layer already exists
build	18-Apr-2018 17:20:36	ae620432889d: Layer already exists
build	18-Apr-2018 17:20:37	a2022691bf95: Layer already exists
build	18-Apr-2018 17:20:37	4685a92e073c: Pushed
build	18-Apr-2018 17:20:38	695eaee0b84c: Pushed
build	18-Apr-2018 17:20:40	browndog_v0.2.0: digest: sha256:e498ced47865dfbf603789504ffd4e791d2553ff6a760e3957a020c866c9b645 size: 3031
build	18-Apr-2018 17:20:40	The push refers to repository [docker.io/clowder/extractors-msc-chemcbc]
build	18-Apr-2018 17:20:41	9ffdd3dc6673: Preparing
build	18-Apr-2018 17:20:41	695eaee0b84c: Preparing
build	18-Apr-2018 17:20:41	4685a92e073c: Preparing
build	18-Apr-2018 17:20:41	1cd7cbd2febc: Preparing
build	18-Apr-2018 17:20:41	0cdb02ac1d86: Preparing
build	18-Apr-2018 17:20:41	f2297bdfc824: Preparing
build	18-Apr-2018 17:20:41	0fbe2bcb1bf9: Preparing
build	18-Apr-2018 17:20:41	59669fcdd5eb: Preparing
build	18-Apr-2018 17:20:41	7f7a065d245a: Preparing
build	18-Apr-2018 17:20:41	f96e6b25195f: Preparing
build	18-Apr-2018 17:20:41	c56153825175: Preparing
build	18-Apr-2018 17:20:41	ae620432889d: Preparing
build	18-Apr-2018 17:20:41	a2022691bf95: Preparing
build	18-Apr-2018 17:20:41	f2297bdfc824: Waiting
build	18-Apr-2018 17:20:41	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:20:41	59669fcdd5eb: Waiting
build	18-Apr-2018 17:20:41	7f7a065d245a: Waiting
build	18-Apr-2018 17:20:41	f96e6b25195f: Waiting
build	18-Apr-2018 17:20:41	c56153825175: Waiting
build	18-Apr-2018 17:20:41	ae620432889d: Waiting
build	18-Apr-2018 17:20:41	a2022691bf95: Waiting
build	18-Apr-2018 17:20:41	9ffdd3dc6673: Layer already exists
build	18-Apr-2018 17:20:41	4685a92e073c: Layer already exists
build	18-Apr-2018 17:20:41	0cdb02ac1d86: Layer already exists
build	18-Apr-2018 17:20:41	695eaee0b84c: Layer already exists
build	18-Apr-2018 17:20:41	1cd7cbd2febc: Layer already exists
build	18-Apr-2018 17:20:41	f2297bdfc824: Layer already exists
build	18-Apr-2018 17:20:41	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:20:41	0fbe2bcb1bf9: Layer already exists
build	18-Apr-2018 17:20:41	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:20:41	a2022691bf95: Layer already exists
build	18-Apr-2018 17:20:41	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:20:41	c56153825175: Layer already exists
build	18-Apr-2018 17:20:41	ae620432889d: Layer already exists
build	18-Apr-2018 17:20:42	browndog_v0.3.0: digest: sha256:e498ced47865dfbf603789504ffd4e791d2553ff6a760e3957a020c866c9b645 size: 3031
build	18-Apr-2018 17:20:42	The push refers to repository [docker.io/clowder/extractors-msc-chemcbc]
build	18-Apr-2018 17:20:42	9ffdd3dc6673: Preparing
build	18-Apr-2018 17:20:42	695eaee0b84c: Preparing
build	18-Apr-2018 17:20:42	4685a92e073c: Preparing
build	18-Apr-2018 17:20:42	1cd7cbd2febc: Preparing
build	18-Apr-2018 17:20:42	0cdb02ac1d86: Preparing
build	18-Apr-2018 17:20:42	f2297bdfc824: Preparing
build	18-Apr-2018 17:20:42	0fbe2bcb1bf9: Preparing
build	18-Apr-2018 17:20:42	59669fcdd5eb: Preparing
build	18-Apr-2018 17:20:42	7f7a065d245a: Preparing
build	18-Apr-2018 17:20:42	f96e6b25195f: Preparing
build	18-Apr-2018 17:20:42	c56153825175: Preparing
build	18-Apr-2018 17:20:42	ae620432889d: Preparing
build	18-Apr-2018 17:20:42	a2022691bf95: Preparing
build	18-Apr-2018 17:20:42	f2297bdfc824: Waiting
build	18-Apr-2018 17:20:42	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:20:42	59669fcdd5eb: Waiting
build	18-Apr-2018 17:20:42	7f7a065d245a: Waiting
build	18-Apr-2018 17:20:42	f96e6b25195f: Waiting
build	18-Apr-2018 17:20:42	c56153825175: Waiting
build	18-Apr-2018 17:20:42	ae620432889d: Waiting
build	18-Apr-2018 17:20:42	a2022691bf95: Waiting
build	18-Apr-2018 17:20:42	9ffdd3dc6673: Layer already exists
build	18-Apr-2018 17:20:42	1cd7cbd2febc: Layer already exists
build	18-Apr-2018 17:20:42	0cdb02ac1d86: Layer already exists
build	18-Apr-2018 17:20:42	695eaee0b84c: Layer already exists
build	18-Apr-2018 17:20:43	4685a92e073c: Layer already exists
build	18-Apr-2018 17:20:43	f2297bdfc824: Layer already exists
build	18-Apr-2018 17:20:43	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:20:43	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:20:43	0fbe2bcb1bf9: Layer already exists
build	18-Apr-2018 17:20:43	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:20:43	c56153825175: Layer already exists
build	18-Apr-2018 17:20:43	ae620432889d: Layer already exists
build	18-Apr-2018 17:20:43	a2022691bf95: Layer already exists
build	18-Apr-2018 17:20:43	latest: digest: sha256:e498ced47865dfbf603789504ffd4e791d2553ff6a760e3957a020c866c9b645 size: 3031
build	18-Apr-2018 17:20:44	Untagged: 17576:latest
build	18-Apr-2018 17:20:44	Sending build context to Docker daemon  198.1kB
build	18-Apr-2018 17:20:44	
build	18-Apr-2018 17:20:44	Step 1/11 : FROM clowder/pyclowder:1
build	18-Apr-2018 17:20:44	 ---> d1a9e970ed30
build	18-Apr-2018 17:20:44	Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu>
build	18-Apr-2018 17:20:44	 ---> Using cache
build	18-Apr-2018 17:20:44	 ---> 46bf81116550
build	18-Apr-2018 17:20:44	Step 3/11 : ENV RABBITMQ_URI=""     RABBITMQ_EXCHANGE="clowder"     RABBITMQ_VHOST="%2F"     RABBITMQ_QUEUE="ncsa.msc.MonitorExtractor"     MONGO_URI=""    DB_USERNAME=""    DB_PASSWORD=""    MAIN_SCRIPT="extractor-Monitor.py"
build	18-Apr-2018 17:20:44	 ---> Running in e2a8df738850
build	18-Apr-2018 17:20:45	Removing intermediate container e2a8df738850
build	18-Apr-2018 17:20:45	 ---> 6612cb4532ae
build	18-Apr-2018 17:20:45	Step 4/11 : USER root
build	18-Apr-2018 17:20:45	 ---> Running in 2533660be846
build	18-Apr-2018 17:20:45	Removing intermediate container 2533660be846
build	18-Apr-2018 17:20:45	 ---> a939e24e5e36
build	18-Apr-2018 17:20:45	Step 5/11 : COPY requirements.txt /home/clowder/
build	18-Apr-2018 17:20:46	 ---> 796505cd296f
build	18-Apr-2018 17:20:46	Step 6/11 : RUN pip install --upgrade pip
build	18-Apr-2018 17:20:46	 ---> Running in c2ad698548d8
build	18-Apr-2018 17:20:48	Collecting pip
build	18-Apr-2018 17:20:48	  Downloading https://files.pythonhosted.org/packages/62/a1/0d452b6901b0157a0134fd27ba89bf95a857fbda64ba52e1ca2cf61d8412/pip-10.0.0-py2.py3-none-any.whl (1.3MB)
build	18-Apr-2018 17:20:48	Installing collected packages: pip
build	18-Apr-2018 17:20:48	  Found existing installation: pip 8.1.1
build	18-Apr-2018 17:20:48	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	18-Apr-2018 17:20:49	Successfully installed pip-10.0.0
build	18-Apr-2018 17:20:51	Removing intermediate container c2ad698548d8
build	18-Apr-2018 17:20:51	 ---> c39deed02ffe
build	18-Apr-2018 17:20:51	Step 7/11 : RUN pip install -r /home/clowder/requirements.txt
build	18-Apr-2018 17:20:51	 ---> Running in d6107ea0681e
build	18-Apr-2018 17:20:52	Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) (1.2.1)
build	18-Apr-2018 17:20:52	Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2))
build	18-Apr-2018 17:20:52	  Downloading https://files.pythonhosted.org/packages/96/53/3782b6cc03500c0949a7ba9dba0c70da95d63d0ed4a04446123987ff983f/openpyxl-1.6.2.tar.gz (199kB)
build	18-Apr-2018 17:20:52	Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3))
build	18-Apr-2018 17:20:52	  Downloading https://files.pythonhosted.org/packages/2b/5b/4c5b6eafc63e0985b926267579a1e2534af70df0a45932f0c23fcc5f1b88/pika-0.9.14.tar.gz (72kB)
build	18-Apr-2018 17:20:53	Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4))
build	18-Apr-2018 17:20:53	  Downloading https://files.pythonhosted.org/packages/d7/94/9aa9ddd3e885caa307c0db8af5a1f5d266d3db44e1ae89bd4e14841ab8d0/pymongo-3.2.1.tar.gz (647kB)
build	18-Apr-2018 17:20:54	Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5))
build	18-Apr-2018 17:20:54	  Downloading https://files.pythonhosted.org/packages/e2/8d/af599c0388f46775c6b039d8b9c4acda2f6ef86787312a35291fff4cb7ca/pytz-2014.3.tar.bz2 (158kB)
build	18-Apr-2018 17:20:54	Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6))
build	18-Apr-2018 17:20:54	  Downloading https://files.pythonhosted.org/packages/7d/15/6efffc6aee666e1456852c2bf1d483b46bf971a2d509b35a98fc3eae1c60/requests-2.2.1-py2.py3-none-any.whl (625kB)
build	18-Apr-2018 17:20:54	Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) (0.1.2)
build	18-Apr-2018 17:20:54	Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8))
build	18-Apr-2018 17:20:54	  Downloading https://files.pythonhosted.org/packages/b1/13/6fbcb55fef0b34c70cb3753741eaafc0e91553a1318653587a7d145caf15/xlrd-0.9.3.tar.gz (178kB)
build	18-Apr-2018 17:20:55	Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd
build	18-Apr-2018 17:20:55	  Running setup.py install for openpyxl: started
build	18-Apr-2018 17:20:55	    Running setup.py install for openpyxl: finished with status 'done'
build	18-Apr-2018 17:20:55	  Found existing installation: pika 0.11.0
build	18-Apr-2018 17:20:55	    Uninstalling pika-0.11.0:
build	18-Apr-2018 17:20:57	      Successfully uninstalled pika-0.11.0
build	18-Apr-2018 17:20:57	  Running setup.py install for pika: started
build	18-Apr-2018 17:20:58	    Running setup.py install for pika: finished with status 'done'
build	18-Apr-2018 17:20:58	  Running setup.py install for pymongo: started
build	18-Apr-2018 17:20:58	    Running setup.py install for pymongo: finished with status 'done'
build	18-Apr-2018 17:20:58	  Running setup.py install for pytz: started
build	18-Apr-2018 17:20:58	    Running setup.py install for pytz: finished with status 'done'
build	18-Apr-2018 17:20:58	  Found existing installation: requests 2.18.4
build	18-Apr-2018 17:20:58	    Uninstalling requests-2.18.4:
build	18-Apr-2018 17:21:01	      Successfully uninstalled requests-2.18.4
build	18-Apr-2018 17:21:01	  Running setup.py install for xlrd: started
build	18-Apr-2018 17:21:01	    Running setup.py install for xlrd: finished with status 'done'
build	18-Apr-2018 17:21:01	Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3
build	18-Apr-2018 17:21:03	Removing intermediate container d6107ea0681e
build	18-Apr-2018 17:21:03	 ---> 980c152d5e6f
build	18-Apr-2018 17:21:03	Step 8/11 : USER clowder
build	18-Apr-2018 17:21:04	 ---> Running in 6352ab3909ce
build	18-Apr-2018 17:21:04	Removing intermediate container 6352ab3909ce
build	18-Apr-2018 17:21:04	 ---> 79d45cc94dda
build	18-Apr-2018 17:21:04	Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/
build	18-Apr-2018 17:21:05	 ---> 8d367fc2568b
build	18-Apr-2018 17:21:05	Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"]
build	18-Apr-2018 17:21:05	 ---> Running in f5e9280dd420
build	18-Apr-2018 17:21:06	Removing intermediate container f5e9280dd420
build	18-Apr-2018 17:21:06	 ---> fd6605ff1eed
build	18-Apr-2018 17:21:06	Step 11/11 : CMD ["extractor"]
build	18-Apr-2018 17:21:06	 ---> Running in 86c76271776b
build	18-Apr-2018 17:21:06	Removing intermediate container 86c76271776b
build	18-Apr-2018 17:21:06	 ---> 11a0c838f3da
build	18-Apr-2018 17:21:06	Successfully built 11a0c838f3da
build	18-Apr-2018 17:21:07	Successfully tagged 17576:latest
build	18-Apr-2018 17:21:07	The push refers to repository [docker.io/clowder/extractors-msc-monitor]
build	18-Apr-2018 17:21:07	630a4020e5d2: Preparing
build	18-Apr-2018 17:21:07	4d32a6daeb31: Preparing
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build	18-Apr-2018 17:21:09	51db3fc7aab4: Pushed
build	18-Apr-2018 17:21:11	55f1d62ecf61: Pushed
build	18-Apr-2018 17:21:14	4d32a6daeb31: Pushed
build	18-Apr-2018 17:21:16	browndog_v0.2.0: digest: sha256:d02b674f2f2d6c69e89b390850093db1ae887220a1daf89ba6881ed7d378b78d size: 3031
build	18-Apr-2018 17:21:17	The push refers to repository [docker.io/clowder/extractors-msc-monitor]
build	18-Apr-2018 17:21:17	630a4020e5d2: Preparing
build	18-Apr-2018 17:21:17	4d32a6daeb31: Preparing
build	18-Apr-2018 17:21:17	55f1d62ecf61: Preparing
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build	18-Apr-2018 17:21:17	f96e6b25195f: Preparing
build	18-Apr-2018 17:21:17	c56153825175: Preparing
build	18-Apr-2018 17:21:17	ae620432889d: Preparing
build	18-Apr-2018 17:21:17	a2022691bf95: Preparing
build	18-Apr-2018 17:21:17	f2297bdfc824: Waiting
build	18-Apr-2018 17:21:17	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:21:17	59669fcdd5eb: Waiting
build	18-Apr-2018 17:21:17	7f7a065d245a: Waiting
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build	18-Apr-2018 17:21:17	ae620432889d: Waiting
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build	18-Apr-2018 17:21:17	ae620432889d: Layer already exists
build	18-Apr-2018 17:21:17	a2022691bf95: Layer already exists
build	18-Apr-2018 17:21:18	browndog_v0.3.0: digest: sha256:d02b674f2f2d6c69e89b390850093db1ae887220a1daf89ba6881ed7d378b78d size: 3031
build	18-Apr-2018 17:21:18	The push refers to repository [docker.io/clowder/extractors-msc-monitor]
build	18-Apr-2018 17:21:19	630a4020e5d2: Preparing
build	18-Apr-2018 17:21:19	4d32a6daeb31: Preparing
build	18-Apr-2018 17:21:19	55f1d62ecf61: Preparing
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build	18-Apr-2018 17:21:19	f96e6b25195f: Preparing
build	18-Apr-2018 17:21:19	c56153825175: Preparing
build	18-Apr-2018 17:21:19	ae620432889d: Preparing
build	18-Apr-2018 17:21:19	a2022691bf95: Preparing
build	18-Apr-2018 17:21:19	7f7a065d245a: Waiting
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build	18-Apr-2018 17:21:19	0fbe2bcb1bf9: Waiting
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build	18-Apr-2018 17:21:19	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:21:19	c56153825175: Layer already exists
build	18-Apr-2018 17:21:19	a2022691bf95: Layer already exists
build	18-Apr-2018 17:21:19	ae620432889d: Layer already exists
build	18-Apr-2018 17:21:20	latest: digest: sha256:d02b674f2f2d6c69e89b390850093db1ae887220a1daf89ba6881ed7d378b78d size: 3031
build	18-Apr-2018 17:21:20	Untagged: 17576:latest
build	18-Apr-2018 17:21:20	Sending build context to Docker daemon   12.1MB
build	18-Apr-2018 17:21:20	
build	18-Apr-2018 17:21:20	Step 1/11 : FROM clowder/pyclowder:1
build	18-Apr-2018 17:21:20	 ---> d1a9e970ed30
build	18-Apr-2018 17:21:20	Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu>
build	18-Apr-2018 17:21:20	 ---> Using cache
build	18-Apr-2018 17:21:20	 ---> 46bf81116550
build	18-Apr-2018 17:21:20	Step 3/11 : ENV RABBITMQ_URI=""     RABBITMQ_EXCHANGE="clowder"     RABBITMQ_VHOST="%2F"     RABBITMQ_QUEUE="ncsa.msc.PhenotypeExtractor"     MONGO_URI=""    DB_USERNAME=""    DB_PASSWORD=""    MAIN_SCRIPT="extractor-Phenotype.py"
build	18-Apr-2018 17:21:21	 ---> Running in fa465fe994cc
build	18-Apr-2018 17:21:21	Removing intermediate container fa465fe994cc
build	18-Apr-2018 17:21:21	 ---> 1604a36dc849
build	18-Apr-2018 17:21:21	Step 4/11 : USER root
build	18-Apr-2018 17:21:21	 ---> Running in e5bf9affb08c
build	18-Apr-2018 17:21:22	Removing intermediate container e5bf9affb08c
build	18-Apr-2018 17:21:22	 ---> c40e6365dcbe
build	18-Apr-2018 17:21:22	Step 5/11 : COPY requirements.txt /home/clowder/
build	18-Apr-2018 17:21:22	 ---> 7fc75f453906
build	18-Apr-2018 17:21:22	Step 6/11 : RUN pip install --upgrade pip
build	18-Apr-2018 17:21:23	 ---> Running in d77eb3868fa8
build	18-Apr-2018 17:21:24	Collecting pip
build	18-Apr-2018 17:21:24	  Downloading https://files.pythonhosted.org/packages/62/a1/0d452b6901b0157a0134fd27ba89bf95a857fbda64ba52e1ca2cf61d8412/pip-10.0.0-py2.py3-none-any.whl (1.3MB)
build	18-Apr-2018 17:21:25	Installing collected packages: pip
build	18-Apr-2018 17:21:25	  Found existing installation: pip 8.1.1
build	18-Apr-2018 17:21:25	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	18-Apr-2018 17:21:25	Successfully installed pip-10.0.0
build	18-Apr-2018 17:21:27	Removing intermediate container d77eb3868fa8
build	18-Apr-2018 17:21:27	 ---> 8df4a7ffb6fb
build	18-Apr-2018 17:21:27	Step 7/11 : RUN pip install -r /home/clowder/requirements.txt
build	18-Apr-2018 17:21:27	 ---> Running in a02673f2ea2f
build	18-Apr-2018 17:21:28	Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) (1.2.1)
build	18-Apr-2018 17:21:28	Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2))
build	18-Apr-2018 17:21:28	  Downloading https://files.pythonhosted.org/packages/96/53/3782b6cc03500c0949a7ba9dba0c70da95d63d0ed4a04446123987ff983f/openpyxl-1.6.2.tar.gz (199kB)
build	18-Apr-2018 17:21:28	Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3))
build	18-Apr-2018 17:21:28	  Downloading https://files.pythonhosted.org/packages/2b/5b/4c5b6eafc63e0985b926267579a1e2534af70df0a45932f0c23fcc5f1b88/pika-0.9.14.tar.gz (72kB)
build	18-Apr-2018 17:21:29	Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4))
build	18-Apr-2018 17:21:29	  Downloading https://files.pythonhosted.org/packages/d7/94/9aa9ddd3e885caa307c0db8af5a1f5d266d3db44e1ae89bd4e14841ab8d0/pymongo-3.2.1.tar.gz (647kB)
build	18-Apr-2018 17:21:30	Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5))
build	18-Apr-2018 17:21:30	  Downloading https://files.pythonhosted.org/packages/e2/8d/af599c0388f46775c6b039d8b9c4acda2f6ef86787312a35291fff4cb7ca/pytz-2014.3.tar.bz2 (158kB)
build	18-Apr-2018 17:21:30	Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6))
build	18-Apr-2018 17:21:30	  Downloading https://files.pythonhosted.org/packages/7d/15/6efffc6aee666e1456852c2bf1d483b46bf971a2d509b35a98fc3eae1c60/requests-2.2.1-py2.py3-none-any.whl (625kB)
build	18-Apr-2018 17:21:30	Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) (0.1.2)
build	18-Apr-2018 17:21:30	Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8))
build	18-Apr-2018 17:21:31	  Downloading https://files.pythonhosted.org/packages/b1/13/6fbcb55fef0b34c70cb3753741eaafc0e91553a1318653587a7d145caf15/xlrd-0.9.3.tar.gz (178kB)
build	18-Apr-2018 17:21:31	Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd
build	18-Apr-2018 17:21:31	  Running setup.py install for openpyxl: started
build	18-Apr-2018 17:21:31	    Running setup.py install for openpyxl: finished with status 'done'
build	18-Apr-2018 17:21:31	  Found existing installation: pika 0.11.0
build	18-Apr-2018 17:21:31	    Uninstalling pika-0.11.0:
build	18-Apr-2018 17:21:34	      Successfully uninstalled pika-0.11.0
build	18-Apr-2018 17:21:34	  Running setup.py install for pika: started
build	18-Apr-2018 17:21:34	    Running setup.py install for pika: finished with status 'done'
build	18-Apr-2018 17:21:34	  Running setup.py install for pymongo: started
build	18-Apr-2018 17:21:35	    Running setup.py install for pymongo: finished with status 'done'
build	18-Apr-2018 17:21:35	  Running setup.py install for pytz: started
build	18-Apr-2018 17:21:35	    Running setup.py install for pytz: finished with status 'done'
build	18-Apr-2018 17:21:35	  Found existing installation: requests 2.18.4
build	18-Apr-2018 17:21:35	    Uninstalling requests-2.18.4:
build	18-Apr-2018 17:21:37	      Successfully uninstalled requests-2.18.4
build	18-Apr-2018 17:21:38	  Running setup.py install for xlrd: started
build	18-Apr-2018 17:21:38	    Running setup.py install for xlrd: finished with status 'done'
build	18-Apr-2018 17:21:38	Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3
build	18-Apr-2018 17:21:40	Removing intermediate container a02673f2ea2f
build	18-Apr-2018 17:21:40	 ---> fd74ef1aceda
build	18-Apr-2018 17:21:40	Step 8/11 : USER clowder
build	18-Apr-2018 17:21:40	 ---> Running in ad21a5e42884
build	18-Apr-2018 17:21:40	Removing intermediate container ad21a5e42884
build	18-Apr-2018 17:21:40	 ---> 630208e60695
build	18-Apr-2018 17:21:40	Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/
build	18-Apr-2018 17:21:42	 ---> 8c7d7ad853eb
build	18-Apr-2018 17:21:42	Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"]
build	18-Apr-2018 17:21:42	 ---> Running in 8e2e188a5eb1
build	18-Apr-2018 17:21:43	Removing intermediate container 8e2e188a5eb1
build	18-Apr-2018 17:21:43	 ---> e585421734f6
build	18-Apr-2018 17:21:43	Step 11/11 : CMD ["extractor"]
build	18-Apr-2018 17:21:43	 ---> Running in d17526fe7b6e
build	18-Apr-2018 17:21:44	Removing intermediate container d17526fe7b6e
build	18-Apr-2018 17:21:44	 ---> 225624e9556a
build	18-Apr-2018 17:21:44	Successfully built 225624e9556a
build	18-Apr-2018 17:21:44	Successfully tagged 17576:latest
build	18-Apr-2018 17:21:44	The push refers to repository [docker.io/clowder/extractors-msc-phenotype]
build	18-Apr-2018 17:21:44	20baf33cf4e5: Preparing
build	18-Apr-2018 17:21:44	67d3d610e020: Preparing
build	18-Apr-2018 17:21:44	b4d78dfb2d96: Preparing
build	18-Apr-2018 17:21:44	764b1463235e: Preparing
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build	18-Apr-2018 17:21:44	ae620432889d: Preparing
build	18-Apr-2018 17:21:44	a2022691bf95: Preparing
build	18-Apr-2018 17:21:44	f2297bdfc824: Waiting
build	18-Apr-2018 17:21:44	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:21:44	59669fcdd5eb: Waiting
build	18-Apr-2018 17:21:44	7f7a065d245a: Waiting
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build	18-Apr-2018 17:21:44	ae620432889d: Waiting
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build	18-Apr-2018 17:21:45	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:21:46	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:21:46	20baf33cf4e5: Pushed
build	18-Apr-2018 17:21:46	c56153825175: Layer already exists
build	18-Apr-2018 17:21:46	764b1463235e: Pushed
build	18-Apr-2018 17:21:46	ae620432889d: Layer already exists
build	18-Apr-2018 17:21:46	a2022691bf95: Layer already exists
build	18-Apr-2018 17:21:47	67d3d610e020: Pushed
build	18-Apr-2018 17:21:47	b4d78dfb2d96: Pushed
build	18-Apr-2018 17:21:50	browndog_v0.2.0: digest: sha256:35428eac474992acdc01a32f6a860e0d5aa4cd9499174b5c6e3c9797a19a19cc size: 3031
build	18-Apr-2018 17:21:51	The push refers to repository [docker.io/clowder/extractors-msc-phenotype]
build	18-Apr-2018 17:21:51	20baf33cf4e5: Preparing
build	18-Apr-2018 17:21:51	67d3d610e020: Preparing
build	18-Apr-2018 17:21:51	b4d78dfb2d96: Preparing
build	18-Apr-2018 17:21:51	764b1463235e: Preparing
build	18-Apr-2018 17:21:51	0cdb02ac1d86: Preparing
build	18-Apr-2018 17:21:51	f2297bdfc824: Preparing
build	18-Apr-2018 17:21:51	0fbe2bcb1bf9: Preparing
build	18-Apr-2018 17:21:51	59669fcdd5eb: Preparing
build	18-Apr-2018 17:21:51	7f7a065d245a: Preparing
build	18-Apr-2018 17:21:51	f96e6b25195f: Preparing
build	18-Apr-2018 17:21:51	c56153825175: Preparing
build	18-Apr-2018 17:21:51	ae620432889d: Preparing
build	18-Apr-2018 17:21:51	a2022691bf95: Preparing
build	18-Apr-2018 17:21:51	f2297bdfc824: Waiting
build	18-Apr-2018 17:21:51	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:21:51	f96e6b25195f: Waiting
build	18-Apr-2018 17:21:51	59669fcdd5eb: Waiting
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build	18-Apr-2018 17:21:51	c56153825175: Waiting
build	18-Apr-2018 17:21:51	b4d78dfb2d96: Layer already exists
build	18-Apr-2018 17:21:51	0cdb02ac1d86: Layer already exists
build	18-Apr-2018 17:21:51	20baf33cf4e5: Layer already exists
build	18-Apr-2018 17:21:51	67d3d610e020: Layer already exists
build	18-Apr-2018 17:21:51	764b1463235e: Layer already exists
build	18-Apr-2018 17:21:51	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:21:51	f2297bdfc824: Layer already exists
build	18-Apr-2018 17:21:51	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:21:51	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:21:51	0fbe2bcb1bf9: Layer already exists
build	18-Apr-2018 17:21:51	c56153825175: Layer already exists
build	18-Apr-2018 17:21:51	ae620432889d: Layer already exists
build	18-Apr-2018 17:21:51	a2022691bf95: Layer already exists
build	18-Apr-2018 17:21:52	browndog_v0.3.0: digest: sha256:35428eac474992acdc01a32f6a860e0d5aa4cd9499174b5c6e3c9797a19a19cc size: 3031
build	18-Apr-2018 17:21:52	The push refers to repository [docker.io/clowder/extractors-msc-phenotype]
build	18-Apr-2018 17:21:52	20baf33cf4e5: Preparing
build	18-Apr-2018 17:21:52	67d3d610e020: Preparing
build	18-Apr-2018 17:21:52	b4d78dfb2d96: Preparing
build	18-Apr-2018 17:21:52	764b1463235e: Preparing
build	18-Apr-2018 17:21:52	0cdb02ac1d86: Preparing
build	18-Apr-2018 17:21:52	f2297bdfc824: Preparing
build	18-Apr-2018 17:21:52	0fbe2bcb1bf9: Preparing
build	18-Apr-2018 17:21:52	59669fcdd5eb: Preparing
build	18-Apr-2018 17:21:52	7f7a065d245a: Preparing
build	18-Apr-2018 17:21:52	f96e6b25195f: Preparing
build	18-Apr-2018 17:21:52	c56153825175: Preparing
build	18-Apr-2018 17:21:52	ae620432889d: Preparing
build	18-Apr-2018 17:21:52	a2022691bf95: Preparing
build	18-Apr-2018 17:21:52	f96e6b25195f: Waiting
build	18-Apr-2018 17:21:52	c56153825175: Waiting
build	18-Apr-2018 17:21:52	59669fcdd5eb: Waiting
build	18-Apr-2018 17:21:52	ae620432889d: Waiting
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build	18-Apr-2018 17:21:52	a2022691bf95: Waiting
build	18-Apr-2018 17:21:52	f2297bdfc824: Waiting
build	18-Apr-2018 17:21:52	0fbe2bcb1bf9: Waiting
build	18-Apr-2018 17:21:53	67d3d610e020: Layer already exists
build	18-Apr-2018 17:21:53	764b1463235e: Layer already exists
build	18-Apr-2018 17:21:53	b4d78dfb2d96: Layer already exists
build	18-Apr-2018 17:21:53	0cdb02ac1d86: Layer already exists
build	18-Apr-2018 17:21:53	20baf33cf4e5: Layer already exists
build	18-Apr-2018 17:21:53	0fbe2bcb1bf9: Layer already exists
build	18-Apr-2018 17:21:53	59669fcdd5eb: Layer already exists
build	18-Apr-2018 17:21:53	f96e6b25195f: Layer already exists
build	18-Apr-2018 17:21:53	f2297bdfc824: Layer already exists
build	18-Apr-2018 17:21:53	7f7a065d245a: Layer already exists
build	18-Apr-2018 17:21:53	ae620432889d: Layer already exists
build	18-Apr-2018 17:21:53	c56153825175: Layer already exists
build	18-Apr-2018 17:21:53	a2022691bf95: Layer already exists
build	18-Apr-2018 17:21:54	latest: digest: sha256:35428eac474992acdc01a32f6a860e0d5aa4cd9499174b5c6e3c9797a19a19cc size: 3031
build	18-Apr-2018 17:21:54	Untagged: 17576:latest
simple	18-Apr-2018 17:21:54	Finished task 'docker build' with result: Success
simple	18-Apr-2018 17:21:54	Running post build plugin 'Docker Container Cleanup'
simple	18-Apr-2018 17:21:54	Running post build plugin 'NCover Results Collector'
simple	18-Apr-2018 17:21:54	Running post build plugin 'Clover Results Collector'
simple	18-Apr-2018 17:21:54	Running post build plugin 'npm Cache Cleanup'
simple	18-Apr-2018 17:21:54	Running post build plugin 'Artifact Copier'
simple	18-Apr-2018 17:21:54	Finalising the build...
simple	18-Apr-2018 17:21:54	Stopping timer.
simple	18-Apr-2018 17:21:54	Build CATS-MSC-JOB1-35 completed.
simple	18-Apr-2018 17:21:54	Running on server: post build plugin 'NCover Results Collector'
simple	18-Apr-2018 17:21:54	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	18-Apr-2018 17:21:54	Running on server: post build plugin 'Clover Delta Calculator'
simple	18-Apr-2018 17:21:54	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	18-Apr-2018 17:21:54	All post build plugins have finished
simple	18-Apr-2018 17:21:54	Generating build results summary...
simple	18-Apr-2018 17:21:54	Saving build results to disk...
simple	18-Apr-2018 17:21:54	Logging substituted variables...
simple	18-Apr-2018 17:21:54	Indexing build results...
simple	18-Apr-2018 17:21:54	Finished building CATS-MSC-JOB1-35.