simple 03-Feb-2017 16:21:43 Build Clowder - extractors-msc - master - Default Job #2 (CATS-MSC1-JOB1-2) started building on agent buildserver-1.ncsa.illinois.edu simple 03-Feb-2017 16:21:43 Remote Agent simple 03-Feb-2017 16:21:43 Build working directory is /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC1-JOB1 simple 03-Feb-2017 16:21:43 Executing build Clowder - extractors-msc - master - Default Job #2 (CATS-MSC1-JOB1-2) simple 03-Feb-2017 16:21:43 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 03-Feb-2017 16:21:43 Updating source code to revision: 85e47c135cd2d896597c8dd58362bfc12d4463d0 simple 03-Feb-2017 16:21:43 Creating local git repository in '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC1-JOB1/.git'. simple 03-Feb-2017 16:21:43 Initialized empty Git repository in /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC1-JOB1/.git/ simple 03-Feb-2017 16:21:44 Fetching 'refs/heads/master' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git'. Will try to do a shallow fetch. simple 03-Feb-2017 16:21:44 Warning: Permanently added '[127.0.0.1]:50740' (RSA) to the list of known hosts. simple 03-Feb-2017 16:21:46 From ssh://127.0.0.1:50740/cats/extractors-msc simple 03-Feb-2017 16:21:46 * [new branch] master -> master simple 03-Feb-2017 16:21:46 Checking out revision 85e47c135cd2d896597c8dd58362bfc12d4463d0. simple 03-Feb-2017 16:21:47 Already on 'master' simple 03-Feb-2017 16:21:47 Updated source code to revision: 85e47c135cd2d896597c8dd58362bfc12d4463d0 simple 03-Feb-2017 16:21:47 Finished task 'Checkout Default Repository' with result: Success simple 03-Feb-2017 16:21:47 Running pre-build action: VCS Version Collector simple 03-Feb-2017 16:21:47 Starting task 'docker build' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 03-Feb-2017 16:21:47 Beginning to execute external process for build 'Clowder - extractors-msc - master - Default Job #2 (CATS-MSC1-JOB1-2)'\n ... running command line: \n/bin/sh docker.sh\n ... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC1-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=master\nbamboo_capability_system_builder_node_Node_js_v6_9_1=/home/bamboo/node-v6.9.1/bin/node\nbamboo_capability_system_builder_command_npm_6=/home/bamboo/node-v6.9.1/bin/npm\nbamboo_capability_system_builder_command_buckminster_4_2=/home/bamboo/buckminster-4.2/buckminster\nbamboo_repository_revision_number=85e47c135cd2d896597c8dd58362bfc12d4463d0\nbamboo_resultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-MSC1-JOB1-2\nbamboo_capability_system_builder_command_sphinx=/usr/bin/sphinx-build\nbamboo_planRepository_1_name=extractors-msc\nbamboo_build_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC1-JOB1\nbamboo_buildKey=CATS-MSC1-JOB1\nbamboo_capability_system_os=linux\nbamboo_shortPlanName=master\nbamboo_repository_127172629_branch_name=master\nbamboo_planRepository_name=extractors-msc\nbamboo_buildNumber=2\nbamboo_capability_system_builder_nodejs_Node_js_v6_9_1=/home/bamboo/node-v6.9.1\nbamboo_capability_system_builder_nodejs_Node_js_v0_10_28=/home/bamboo/node-v0.10.28\nbamboo_repository_127172629_git_username=\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-MSC1-JOB1-2\nbamboo_planRepository_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git\nbamboo_agentId=108560385\nbamboo_planName=Clowder - extractors-msc - master\nbamboo_shortPlanKey=MSC1\nbamboo_capability_system_builder_command_sbt_0_13=/home/bamboo/sbt-0.13.2/bin/sbt\nbamboo_repository_127172629_git_branch=master\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_builder_node_Node_js_v0_10_28=/home/bamboo/node-v0.10.28/bin/node\nbamboo_repository_127172629_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git\nbamboo_repository_127172629_name=extractors-msc\nbamboo_planRepository_revision=85e47c135cd2d896597c8dd58362bfc12d4463d0\nbamboo_repository_previous_revision_number=fcb4e1a54dea0bccc7c1e15742a71aeb43a25c5c\nbamboo_buildTimeStamp=2017-02-03T16:20:04.396-06:00\nbamboo_capability_system_builder_command_npm=/home/bamboo/node-v0.10.28/bin/npm\nbamboo_planRepository_previousRevision=fcb4e1a54dea0bccc7c1e15742a71aeb43a25c5c\nbamboo_capability_system_builder_mvn2_Maven_2=/home/bamboo/apache-maven-2.2.1\nbamboo_buildResultKey=CATS-MSC1-JOB1-2\nbamboo_repository_git_branch=master\nbamboo_repository_branch_name=master\nbamboo_buildPlanName=Clowder - extractors-msc - master - Default Job\nbamboo_planRepository_1_revision=85e47c135cd2d896597c8dd58362bfc12d4463d0\nbamboo_capability_system_builder_command_python3=/usr/bin/python3\nbamboo_repository_name=extractors-msc\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_planRepository_1_previousRevision=fcb4e1a54dea0bccc7c1e15742a71aeb43a25c5c\nbamboo_repository_git_username=\nbamboo_capability_system_builder_sbt_SBT_0_13_13=/home/bamboo/sbt-0.13.13\nbamboo_capability_system_builder_command_phantomjs=/home/bamboo/phantomjs-1.9.8/bin/phantomjs\nbamboo_planRepository_1_type=stash-rep\nbamboo_planRepository_branchName=master\nbamboo_capability_system_builder_command_python2_7=/usr/bin/python2.7\nbamboo_repository_127172629_previous_revision_number=fcb4e1a54dea0bccc7c1e15742a71aeb43a25c5c\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_capability_system_software_rabbitmq=/usr/sbin/rabbitmqctl\nbamboo_capability_system_builder_command_casperjs=/home/bamboo/node-v0.10.28/bin/casperjs\nbamboo_planRepository_type=stash-rep\nbamboo_planRepository_1_username=\nbamboo_capability_system_jdk_JDK_1_8_0_66=/home/bamboo/jdk1.8.0_66\nbamboo_repository_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_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC1-JOB1\nbamboo_planKey=CATS-MSC1\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_planRepository_1_branchName=master\nbamboo_repository_127172629_revision_number=85e47c135cd2d896597c8dd58362bfc12d4463d0\n build 03-Feb-2017 16:21:47 Sending build context to Docker daemon 557.1 kB build 03-Feb-2017 16:21:47 Sending build context to Docker daemon 1.114 MB build 03-Feb-2017 16:21:47 Sending build context to Docker daemon 1.671 MB build 03-Feb-2017 16:21:47 Sending build context to Docker daemon 2.228 MB build 03-Feb-2017 16:21:47 Sending build context to Docker daemon 2.284 MB build 03-Feb-2017 16:21:47 build 03-Feb-2017 16:21:47 Step 1 : FROM clowder/pyclowder:1 build 03-Feb-2017 16:21:47 ---> 2dd17798784b build 03-Feb-2017 16:21:47 Step 2 : MAINTAINER Rob Kooper build 03-Feb-2017 16:21:47 ---> Using cache build 03-Feb-2017 16:21:47 ---> 07579dbf21e8 build 03-Feb-2017 16:21:47 Step 3 : VOLUME /matlab build 03-Feb-2017 16:21:47 ---> Using cache build 03-Feb-2017 16:21:47 ---> fbba1206c292 build 03-Feb-2017 16:21:47 Step 4 : ENV RABBITMQ_URI "" RABBITMQ_EXCHANGE "clowder" RABBITMQ_VHOST "%2F" RABBITMQ_QUEUE "ncsa.msc.diagnosis" MATLAB_BINARY "/matlab/bin/matlab" MAIN_SCRIPT "diagnosis.py" build 03-Feb-2017 16:21:47 ---> Running in e200017be798 build 03-Feb-2017 16:21:47 ---> c22d618a5453 build 03-Feb-2017 16:21:47 Removing intermediate container e200017be798 build 03-Feb-2017 16:21:47 Step 5 : USER root build 03-Feb-2017 16:21:47 ---> Running in 02e69047d47f build 03-Feb-2017 16:21:47 ---> 801367e9bc50 build 03-Feb-2017 16:21:47 Removing intermediate container 02e69047d47f build 03-Feb-2017 16:21:47 Step 6 : RUN pip install --upgrade pip build 03-Feb-2017 16:21:47 ---> Running in 30e91f46aff7 build 03-Feb-2017 16:21:50 Collecting pip build 03-Feb-2017 16:21:51 Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB) build 03-Feb-2017 16:21:51 Installing collected packages: pip build 03-Feb-2017 16:21:51 Found existing installation: pip 8.1.1 build 03-Feb-2017 16:21:51 Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr build 03-Feb-2017 16:21:53 Successfully installed pip-9.0.1 build 03-Feb-2017 16:21:53 ---> 26a2f7e6e919 build 03-Feb-2017 16:21:54 Removing intermediate container 30e91f46aff7 build 03-Feb-2017 16:21:54 Step 7 : RUN apt-get -qq -y update && apt-get -y install libxext6 libxmu6 libxt6 wget && mkdir -p /matlab && rm -rf /var/lib/apt/lists/* build 03-Feb-2017 16:21:54 ---> Running in af2cd25d3d90 build 03-Feb-2017 16:22:02 Reading package lists... build 03-Feb-2017 16:22:02 Building dependency tree... build 03-Feb-2017 16:22:02 Reading state information... build 03-Feb-2017 16:22:03 The following additional packages will be installed: build 03-Feb-2017 16:22:03 libice6 libidn11 libsm6 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 build 03-Feb-2017 16:22:03 x11-common build 03-Feb-2017 16:22:03 The following NEW packages will be installed: build 03-Feb-2017 16:22:03 libice6 libidn11 libsm6 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 build 03-Feb-2017 16:22:03 libxext6 libxmu6 libxt6 wget x11-common build 03-Feb-2017 16:22:03 0 upgraded, 13 newly installed, 0 to remove and 6 not upgraded. build 03-Feb-2017 16:22:03 Need to get 1401 kB of archives. build 03-Feb-2017 16:22:03 After this operation, 5592 kB of additional disk space will be used. build 03-Feb-2017 16:22:03 Get:1 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B] build 03-Feb-2017 16:22:03 Get:2 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [11.0 kB] build 03-Feb-2017 16:22:03 Get:3 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxcb1 amd64 1.11.1-1ubuntu1 [40.0 kB] build 03-Feb-2017 16:22:03 Get:4 http://archive.ubuntu.com/ubuntu xenial/main amd64 libx11-data all 2:1.6.3-1ubuntu2 [113 kB] build 03-Feb-2017 16:22:03 Get:5 http://archive.ubuntu.com/ubuntu xenial/main amd64 libx11-6 amd64 2:1.6.3-1ubuntu2 [571 kB] build 03-Feb-2017 16:22:04 Get:6 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB] build 03-Feb-2017 16:22:04 Get:7 http://archive.ubuntu.com/ubuntu xenial/main amd64 x11-common all 1:7.7+13ubuntu3 [22.4 kB] build 03-Feb-2017 16:22:04 Get:8 http://archive.ubuntu.com/ubuntu xenial/main amd64 libice6 amd64 2:1.0.9-1 [39.2 kB] build 03-Feb-2017 16:22:04 Get:9 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB] build 03-Feb-2017 16:22:04 Get:10 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libidn11 amd64 1.32-3ubuntu1.1 [45.6 kB] build 03-Feb-2017 16:22:04 Get:11 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 wget amd64 1.17.1-1ubuntu1.1 [298 kB] build 03-Feb-2017 16:22:04 Get:12 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxt6 amd64 1:1.1.5-0ubuntu1 [160 kB] build 03-Feb-2017 16:22:04 Get:13 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxmu6 amd64 2:1.1.2-2 [46.0 kB] build 03-Feb-2017 16:22:04 debconf: delaying package configuration, since apt-utils is not installed build 03-Feb-2017 16:22:04 Fetched 1401 kB in 1s (1197 kB/s) build 03-Feb-2017 16:22:04 Selecting previously unselected package libxau6:amd64. build 03-Feb-2017 16:22:04 (Reading database ... build 03-Feb-2017 16:22:04 (Reading database ... 5% build 03-Feb-2017 16:22:04 (Reading database ... 10% build 03-Feb-2017 16:22:04 (Reading database ... 15% build 03-Feb-2017 16:22:04 (Reading database ... 20% build 03-Feb-2017 16:22:04 (Reading database ... 25% build 03-Feb-2017 16:22:04 (Reading database ... 30% build 03-Feb-2017 16:22:04 (Reading database ... 35% build 03-Feb-2017 16:22:04 (Reading database ... 40% build 03-Feb-2017 16:22:04 (Reading database ... 45% build 03-Feb-2017 16:22:04 (Reading database ... 50% build 03-Feb-2017 16:22:04 (Reading database ... 55% build 03-Feb-2017 16:22:04 (Reading database ... 60% build 03-Feb-2017 16:22:04 (Reading database ... 65% build 03-Feb-2017 16:22:04 (Reading database ... 70% build 03-Feb-2017 16:22:04 (Reading database ... 75% build 03-Feb-2017 16:22:04 (Reading database ... 80% build 03-Feb-2017 16:22:04 (Reading database ... 85% build 03-Feb-2017 16:22:04 (Reading database ... 90% build 03-Feb-2017 16:22:04 (Reading database ... 95% build 03-Feb-2017 16:22:04 (Reading database ... 100% build 03-Feb-2017 16:22:04 (Reading database ... 8589 files and directories currently installed.) build 03-Feb-2017 16:22:04 Preparing to unpack .../libxau6_1%3a1.0.8-1_amd64.deb ... build 03-Feb-2017 16:22:04 Unpacking libxau6:amd64 (1:1.0.8-1) ... build 03-Feb-2017 16:22:04 Selecting previously unselected package libxdmcp6:amd64. build 03-Feb-2017 16:22:04 Preparing to unpack .../libxdmcp6_1%3a1.1.2-1.1_amd64.deb ... build 03-Feb-2017 16:22:04 Unpacking libxdmcp6:amd64 (1:1.1.2-1.1) ... build 03-Feb-2017 16:22:04 Selecting previously unselected package libxcb1:amd64. build 03-Feb-2017 16:22:04 Preparing to unpack .../libxcb1_1.11.1-1ubuntu1_amd64.deb ... build 03-Feb-2017 16:22:04 Unpacking libxcb1:amd64 (1.11.1-1ubuntu1) ... build 03-Feb-2017 16:22:04 Selecting previously unselected package libx11-data. build 03-Feb-2017 16:22:04 Preparing to unpack .../libx11-data_2%3a1.6.3-1ubuntu2_all.deb ... build 03-Feb-2017 16:22:04 Unpacking libx11-data (2:1.6.3-1ubuntu2) ... build 03-Feb-2017 16:22:05 Selecting previously unselected package libx11-6:amd64. build 03-Feb-2017 16:22:05 Preparing to unpack .../libx11-6_2%3a1.6.3-1ubuntu2_amd64.deb ... build 03-Feb-2017 16:22:05 Unpacking libx11-6:amd64 (2:1.6.3-1ubuntu2) ... build 03-Feb-2017 16:22:05 Selecting previously unselected package libxext6:amd64. build 03-Feb-2017 16:22:05 Preparing to unpack .../libxext6_2%3a1.3.3-1_amd64.deb ... build 03-Feb-2017 16:22:05 Unpacking libxext6:amd64 (2:1.3.3-1) ... build 03-Feb-2017 16:22:05 Selecting previously unselected package x11-common. build 03-Feb-2017 16:22:05 Preparing to unpack .../x11-common_1%3a7.7+13ubuntu3_all.deb ... build 03-Feb-2017 16:22:05 Unpacking x11-common (1:7.7+13ubuntu3) ... build 03-Feb-2017 16:22:05 Selecting previously unselected package libice6:amd64. build 03-Feb-2017 16:22:05 Preparing to unpack .../libice6_2%3a1.0.9-1_amd64.deb ... build 03-Feb-2017 16:22:05 Unpacking libice6:amd64 (2:1.0.9-1) ... build 03-Feb-2017 16:22:05 Selecting previously unselected package libsm6:amd64. build 03-Feb-2017 16:22:05 Preparing to unpack .../libsm6_2%3a1.2.2-1_amd64.deb ... build 03-Feb-2017 16:22:05 Unpacking libsm6:amd64 (2:1.2.2-1) ... build 03-Feb-2017 16:22:05 Selecting previously unselected package libidn11:amd64. build 03-Feb-2017 16:22:05 Preparing to unpack .../libidn11_1.32-3ubuntu1.1_amd64.deb ... build 03-Feb-2017 16:22:05 Unpacking libidn11:amd64 (1.32-3ubuntu1.1) ... build 03-Feb-2017 16:22:05 Selecting previously unselected package wget. build 03-Feb-2017 16:22:05 Preparing to unpack .../wget_1.17.1-1ubuntu1.1_amd64.deb ... build 03-Feb-2017 16:22:05 Unpacking wget (1.17.1-1ubuntu1.1) ... build 03-Feb-2017 16:22:05 Selecting previously unselected package libxt6:amd64. build 03-Feb-2017 16:22:05 Preparing to unpack .../libxt6_1%3a1.1.5-0ubuntu1_amd64.deb ... build 03-Feb-2017 16:22:05 Unpacking libxt6:amd64 (1:1.1.5-0ubuntu1) ... build 03-Feb-2017 16:22:05 Selecting previously unselected package libxmu6:amd64. build 03-Feb-2017 16:22:05 Preparing to unpack .../libxmu6_2%3a1.1.2-2_amd64.deb ... build 03-Feb-2017 16:22:05 Unpacking libxmu6:amd64 (2:1.1.2-2) ... build 03-Feb-2017 16:22:05 Processing triggers for libc-bin (2.23-0ubuntu5) ... build 03-Feb-2017 16:22:05 Processing triggers for systemd (229-4ubuntu13) ... build 03-Feb-2017 16:22:05 Setting up libxau6:amd64 (1:1.0.8-1) ... build 03-Feb-2017 16:22:05 Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ... build 03-Feb-2017 16:22:05 Setting up libxcb1:amd64 (1.11.1-1ubuntu1) ... build 03-Feb-2017 16:22:05 Setting up libx11-data (2:1.6.3-1ubuntu2) ... build 03-Feb-2017 16:22:05 Setting up libx11-6:amd64 (2:1.6.3-1ubuntu2) ... build 03-Feb-2017 16:22:05 Setting up libxext6:amd64 (2:1.3.3-1) ... build 03-Feb-2017 16:22:05 Setting up x11-common (1:7.7+13ubuntu3) ... build 03-Feb-2017 16:22:06 debconf: unable to initialize frontend: Dialog build 03-Feb-2017 16:22:06 debconf: (TERM is not set, so the dialog frontend is not usable.) build 03-Feb-2017 16:22:06 debconf: falling back to frontend: Readline build 03-Feb-2017 16:22:06 debconf: unable to initialize frontend: Readline build 03-Feb-2017 16:22:06 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 03-Feb-2017 16:22:06 debconf: falling back to frontend: Teletype build 03-Feb-2017 16:22:06 update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults build 03-Feb-2017 16:22:06 invoke-rc.d: could not determine current runlevel build 03-Feb-2017 16:22:06 invoke-rc.d: policy-rc.d denied execution of start. build 03-Feb-2017 16:22:06 Setting up libice6:amd64 (2:1.0.9-1) ... build 03-Feb-2017 16:22:06 Setting up libsm6:amd64 (2:1.2.2-1) ... build 03-Feb-2017 16:22:06 Setting up libidn11:amd64 (1.32-3ubuntu1.1) ... build 03-Feb-2017 16:22:06 Setting up wget (1.17.1-1ubuntu1.1) ... build 03-Feb-2017 16:22:06 Setting up libxt6:amd64 (1:1.1.5-0ubuntu1) ... build 03-Feb-2017 16:22:06 Setting up libxmu6:amd64 (2:1.1.2-2) ... build 03-Feb-2017 16:22:06 Processing triggers for libc-bin (2.23-0ubuntu5) ... build 03-Feb-2017 16:22:06 Processing triggers for systemd (229-4ubuntu13) ... build 03-Feb-2017 16:22:07 ---> 55c8f1043ff6 build 03-Feb-2017 16:22:07 Removing intermediate container af2cd25d3d90 build 03-Feb-2017 16:22:07 Step 8 : USER clowder build 03-Feb-2017 16:22:07 ---> Running in 175fea624bf8 build 03-Feb-2017 16:22:07 ---> 6fbeea08ecf9 build 03-Feb-2017 16:22:07 Removing intermediate container 175fea624bf8 build 03-Feb-2017 16:22:07 Step 9 : COPY entrypoint.sh *.py *.m data/*.mat *.json /home/clowder/ build 03-Feb-2017 16:22:09 ---> ca3bdb6ce592 build 03-Feb-2017 16:22:09 Removing intermediate container 453c9ce6ee83 build 03-Feb-2017 16:22:09 Step 10 : ENTRYPOINT /home/clowder/entrypoint.sh build 03-Feb-2017 16:22:09 ---> Running in 49e09f1f0094 build 03-Feb-2017 16:22:09 ---> cdac4e026568 build 03-Feb-2017 16:22:09 Removing intermediate container 49e09f1f0094 build 03-Feb-2017 16:22:09 Step 11 : CMD extractor build 03-Feb-2017 16:22:09 ---> Running in 6f54210164d3 build 03-Feb-2017 16:22:09 ---> 7cc2f1ad0e35 build 03-Feb-2017 16:22:09 Removing intermediate container 6f54210164d3 build 03-Feb-2017 16:22:09 Successfully built 7cc2f1ad0e35 build 03-Feb-2017 16:22:09 The push refers to a repository [docker.io/clowder/extractors-msc-kidney] build 03-Feb-2017 16:22:09 8a808f219b40: Preparing build 03-Feb-2017 16:22:09 7495ec0c9cb3: Preparing build 03-Feb-2017 16:22:09 f8b0aab61870: Preparing build 03-Feb-2017 16:22:09 5e269aa11a2f: Preparing build 03-Feb-2017 16:22:09 7d760664bbad: Preparing build 03-Feb-2017 16:22:09 a2688f6622a7: Preparing build 03-Feb-2017 16:22:09 e24a372680fc: Preparing build 03-Feb-2017 16:22:09 5eb5bd4c5014: Preparing build 03-Feb-2017 16:22:09 d195a7a18c70: Preparing build 03-Feb-2017 16:22:09 af605e724c5a: Preparing build 03-Feb-2017 16:22:09 59f161c3069d: Preparing build 03-Feb-2017 16:22:09 4f03495a4d7d: Preparing build 03-Feb-2017 16:22:09 a2688f6622a7: Waiting build 03-Feb-2017 16:22:09 e24a372680fc: Waiting build 03-Feb-2017 16:22:09 5eb5bd4c5014: Waiting build 03-Feb-2017 16:22:09 d195a7a18c70: Waiting build 03-Feb-2017 16:22:09 af605e724c5a: Waiting build 03-Feb-2017 16:22:09 59f161c3069d: Waiting build 03-Feb-2017 16:22:09 4f03495a4d7d: Waiting build 03-Feb-2017 16:22:11 7d760664bbad: Mounted from clowder/extractors-river build 03-Feb-2017 16:22:11 a2688f6622a7: Mounted from clowder/extractors-river build 03-Feb-2017 16:22:11 5e269aa11a2f: Mounted from clowder/extractors-river build 03-Feb-2017 16:22:12 e24a372680fc: Mounted from clowder/extractors-river build 03-Feb-2017 16:22:12 8a808f219b40: Pushed build 03-Feb-2017 16:22:12 5eb5bd4c5014: Mounted from clowder/extractors-river build 03-Feb-2017 16:22:12 d195a7a18c70: Mounted from clowder/extractors-river build 03-Feb-2017 16:22:12 af605e724c5a: Mounted from clowder/extractors-river build 03-Feb-2017 16:22:12 59f161c3069d: Mounted from clowder/extractors-river build 03-Feb-2017 16:22:12 4f03495a4d7d: Mounted from clowder/extractors-river build 03-Feb-2017 16:22:13 f8b0aab61870: Pushed build 03-Feb-2017 16:22:13 7495ec0c9cb3: Pushed build 03-Feb-2017 16:22:16 master: digest: sha256:40a1059439c3b71a11cae3a63d854209dcf5bf1efe9e66f164d8e77d30258e6f size: 2826 build 03-Feb-2017 16:22:16 The push refers to a repository [docker.io/clowder/extractors-msc-kidney] build 03-Feb-2017 16:22:16 8a808f219b40: Preparing build 03-Feb-2017 16:22:16 7495ec0c9cb3: Preparing build 03-Feb-2017 16:22:16 f8b0aab61870: Preparing build 03-Feb-2017 16:22:16 5e269aa11a2f: Preparing build 03-Feb-2017 16:22:16 7d760664bbad: Preparing build 03-Feb-2017 16:22:16 a2688f6622a7: Preparing build 03-Feb-2017 16:22:16 e24a372680fc: Preparing build 03-Feb-2017 16:22:16 5eb5bd4c5014: Preparing build 03-Feb-2017 16:22:16 d195a7a18c70: Preparing build 03-Feb-2017 16:22:16 af605e724c5a: Preparing build 03-Feb-2017 16:22:16 59f161c3069d: Preparing build 03-Feb-2017 16:22:16 4f03495a4d7d: Preparing build 03-Feb-2017 16:22:16 a2688f6622a7: Waiting build 03-Feb-2017 16:22:16 e24a372680fc: Waiting build 03-Feb-2017 16:22:16 5eb5bd4c5014: Waiting build 03-Feb-2017 16:22:16 d195a7a18c70: Waiting build 03-Feb-2017 16:22:16 af605e724c5a: Waiting build 03-Feb-2017 16:22:16 4f03495a4d7d: Waiting build 03-Feb-2017 16:22:16 8a808f219b40: Layer already exists build 03-Feb-2017 16:22:16 5e269aa11a2f: Layer already exists build 03-Feb-2017 16:22:16 7495ec0c9cb3: Layer already exists build 03-Feb-2017 16:22:16 f8b0aab61870: Layer already exists build 03-Feb-2017 16:22:16 7d760664bbad: Layer already exists build 03-Feb-2017 16:22:16 a2688f6622a7: Layer already exists build 03-Feb-2017 16:22:16 e24a372680fc: Layer already exists build 03-Feb-2017 16:22:16 5eb5bd4c5014: Layer already exists build 03-Feb-2017 16:22:16 af605e724c5a: Layer already exists build 03-Feb-2017 16:22:16 d195a7a18c70: Layer already exists build 03-Feb-2017 16:22:17 4f03495a4d7d: Layer already exists build 03-Feb-2017 16:22:17 59f161c3069d: Layer already exists build 03-Feb-2017 16:22:17 latest: digest: sha256:40a1059439c3b71a11cae3a63d854209dcf5bf1efe9e66f164d8e77d30258e6f size: 2826 build 03-Feb-2017 16:22:17 Untagged: 23804:latest build 03-Feb-2017 16:22:17 Sending build context to Docker daemon 67.07 kB build 03-Feb-2017 16:22:17 build 03-Feb-2017 16:22:17 Step 1 : FROM clowder/pyclowder:1 build 03-Feb-2017 16:22:17 ---> 2dd17798784b build 03-Feb-2017 16:22:17 Step 2 : MAINTAINER Yan Zhao build 03-Feb-2017 16:22:17 ---> Running in 27d7df551b94 build 03-Feb-2017 16:22:17 ---> 2c58a262fb36 build 03-Feb-2017 16:22:17 Removing intermediate container 27d7df551b94 build 03-Feb-2017 16:22:17 Step 3 : 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 03-Feb-2017 16:22:17 ---> Running in cd32127a3280 build 03-Feb-2017 16:22:17 ---> 6911c7601ef2 build 03-Feb-2017 16:22:17 Removing intermediate container cd32127a3280 build 03-Feb-2017 16:22:17 Step 4 : USER root build 03-Feb-2017 16:22:18 ---> Running in b281f139c46a build 03-Feb-2017 16:22:18 ---> 53b8142f6241 build 03-Feb-2017 16:22:18 Removing intermediate container b281f139c46a build 03-Feb-2017 16:22:18 Step 5 : COPY requirements.txt /home/clowder/ build 03-Feb-2017 16:22:18 ---> 4998e1378f2c build 03-Feb-2017 16:22:18 Removing intermediate container 1f5e38571ec2 build 03-Feb-2017 16:22:18 Step 6 : RUN pip install --upgrade pip build 03-Feb-2017 16:22:18 ---> Running in c0623c0b7ed3 build 03-Feb-2017 16:22:20 Collecting pip build 03-Feb-2017 16:22:20 Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB) build 03-Feb-2017 16:22:21 Installing collected packages: pip build 03-Feb-2017 16:22:21 Found existing installation: pip 8.1.1 build 03-Feb-2017 16:22:21 Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr build 03-Feb-2017 16:22:22 Successfully installed pip-9.0.1 build 03-Feb-2017 16:22:23 ---> 8f7fa9e616ea build 03-Feb-2017 16:22:23 Removing intermediate container c0623c0b7ed3 build 03-Feb-2017 16:22:23 Step 7 : RUN pip install -r /home/clowder/requirements.txt build 03-Feb-2017 16:22:23 ---> Running in a3b87e351eb5 build 03-Feb-2017 16:22:24 Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) build 03-Feb-2017 16:22:24 Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2)) build 03-Feb-2017 16:22:24 Downloading openpyxl-1.6.2.tar.gz (199kB) build 03-Feb-2017 16:22:27 Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3)) build 03-Feb-2017 16:22:27 Downloading pika-0.9.14.tar.gz (72kB) build 03-Feb-2017 16:22:28 Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4)) build 03-Feb-2017 16:22:28 Downloading pymongo-3.2.1.tar.gz (647kB) build 03-Feb-2017 16:22:29 Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5)) build 03-Feb-2017 16:22:30 Downloading pytz-2014.3.zip (482kB) build 03-Feb-2017 16:22:31 Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6)) build 03-Feb-2017 16:22:31 Downloading requests-2.2.1-py2.py3-none-any.whl (625kB) build 03-Feb-2017 16:22:31 Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) build 03-Feb-2017 16:22:31 Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8)) build 03-Feb-2017 16:22:31 Downloading xlrd-0.9.3.tar.gz (178kB) build 03-Feb-2017 16:22:32 Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd build 03-Feb-2017 16:22:32 Running setup.py install for openpyxl: started build 03-Feb-2017 16:22:33 Running setup.py install for openpyxl: finished with status 'done' build 03-Feb-2017 16:22:33 Found existing installation: pika 0.10.0 build 03-Feb-2017 16:22:33 Uninstalling pika-0.10.0: build 03-Feb-2017 16:22:33 Successfully uninstalled pika-0.10.0 build 03-Feb-2017 16:22:33 Running setup.py install for pika: started build 03-Feb-2017 16:22:34 Running setup.py install for pika: finished with status 'done' build 03-Feb-2017 16:22:34 Running setup.py install for pymongo: started build 03-Feb-2017 16:22:35 Running setup.py install for pymongo: finished with status 'done' build 03-Feb-2017 16:22:35 Running setup.py install for pytz: started build 03-Feb-2017 16:22:36 Running setup.py install for pytz: finished with status 'done' build 03-Feb-2017 16:22:36 Found existing installation: requests 2.13.0 build 03-Feb-2017 16:22:36 Uninstalling requests-2.13.0: build 03-Feb-2017 16:22:37 Successfully uninstalled requests-2.13.0 build 03-Feb-2017 16:22:38 Running setup.py install for xlrd: started build 03-Feb-2017 16:22:39 Running setup.py install for xlrd: finished with status 'done' build 03-Feb-2017 16:22:39 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 03-Feb-2017 16:22:40 ---> 9a4d4d6eb343 build 03-Feb-2017 16:22:40 Removing intermediate container a3b87e351eb5 build 03-Feb-2017 16:22:40 Step 8 : USER clowder build 03-Feb-2017 16:22:40 ---> Running in 9439dac1f895 build 03-Feb-2017 16:22:41 ---> e6adda8501eb build 03-Feb-2017 16:22:41 Removing intermediate container 9439dac1f895 build 03-Feb-2017 16:22:41 Step 9 : COPY entrypoint.sh *.py *.json /home/clowder/ build 03-Feb-2017 16:22:42 ---> f13531308d2a build 03-Feb-2017 16:22:42 Removing intermediate container 1f7b5ef03efa build 03-Feb-2017 16:22:42 Step 10 : ENTRYPOINT /home/clowder/entrypoint.sh build 03-Feb-2017 16:22:42 ---> Running in 1342430d477a build 03-Feb-2017 16:22:42 ---> 638dcd570617 build 03-Feb-2017 16:22:42 Removing intermediate container 1342430d477a build 03-Feb-2017 16:22:42 Step 11 : CMD extractor build 03-Feb-2017 16:22:42 ---> Running in 2cd7ee76ad1c build 03-Feb-2017 16:22:42 ---> c421ece5c86c build 03-Feb-2017 16:22:42 Removing intermediate container 2cd7ee76ad1c build 03-Feb-2017 16:22:42 Successfully built c421ece5c86c build 03-Feb-2017 16:22:42 The push refers to a repository [docker.io/clowder/extractors-msc-islet] build 03-Feb-2017 16:22:42 a3a514ba80a3: Preparing build 03-Feb-2017 16:22:42 bfc8a6a4f87c: Preparing build 03-Feb-2017 16:22:42 a31423c85135: Preparing build 03-Feb-2017 16:22:42 dce1077ded56: Preparing build 03-Feb-2017 16:22:42 5e269aa11a2f: Preparing build 03-Feb-2017 16:22:42 7d760664bbad: Preparing build 03-Feb-2017 16:22:42 a2688f6622a7: Preparing build 03-Feb-2017 16:22:42 e24a372680fc: Preparing build 03-Feb-2017 16:22:42 5eb5bd4c5014: Preparing build 03-Feb-2017 16:22:42 d195a7a18c70: Preparing build 03-Feb-2017 16:22:42 af605e724c5a: Preparing build 03-Feb-2017 16:22:42 59f161c3069d: Preparing build 03-Feb-2017 16:22:42 4f03495a4d7d: Preparing build 03-Feb-2017 16:22:42 7d760664bbad: Waiting build 03-Feb-2017 16:22:42 a2688f6622a7: Waiting build 03-Feb-2017 16:22:42 e24a372680fc: Waiting build 03-Feb-2017 16:22:42 5eb5bd4c5014: Waiting build 03-Feb-2017 16:22:42 d195a7a18c70: Waiting build 03-Feb-2017 16:22:42 af605e724c5a: Waiting build 03-Feb-2017 16:22:42 59f161c3069d: Waiting build 03-Feb-2017 16:22:42 4f03495a4d7d: Waiting build 03-Feb-2017 16:22:43 5e269aa11a2f: Mounted from clowder/extractors-msc-kidney build 03-Feb-2017 16:22:44 7d760664bbad: Mounted from clowder/extractors-msc-kidney build 03-Feb-2017 16:22:45 a2688f6622a7: Mounted from clowder/extractors-msc-kidney build 03-Feb-2017 16:22:45 dce1077ded56: Pushed build 03-Feb-2017 16:22:45 e24a372680fc: Mounted from clowder/extractors-msc-kidney build 03-Feb-2017 16:22:46 5eb5bd4c5014: Mounted from clowder/extractors-msc-kidney build 03-Feb-2017 16:22:46 a3a514ba80a3: Pushed build 03-Feb-2017 16:22:46 d195a7a18c70: Mounted from clowder/extractors-msc-kidney build 03-Feb-2017 16:22:46 af605e724c5a: Mounted from clowder/extractors-msc-kidney build 03-Feb-2017 16:22:46 59f161c3069d: Mounted from clowder/extractors-msc-kidney build 03-Feb-2017 16:22:46 4f03495a4d7d: Mounted from clowder/extractors-msc-kidney build 03-Feb-2017 16:22:47 bfc8a6a4f87c: Pushed build 03-Feb-2017 16:22:47 a31423c85135: Pushed build 03-Feb-2017 16:22:50 master: digest: sha256:d6824ae03568dc8e5aa5d2d6ed336c51556b632d695e60f8c14a31ab1f5324a7 size: 3031 build 03-Feb-2017 16:22:50 The push refers to a repository [docker.io/clowder/extractors-msc-islet] build 03-Feb-2017 16:22:50 a3a514ba80a3: Preparing build 03-Feb-2017 16:22:50 bfc8a6a4f87c: Preparing build 03-Feb-2017 16:22:50 a31423c85135: Preparing build 03-Feb-2017 16:22:50 dce1077ded56: Preparing build 03-Feb-2017 16:22:50 5e269aa11a2f: Preparing build 03-Feb-2017 16:22:50 7d760664bbad: Preparing build 03-Feb-2017 16:22:50 a2688f6622a7: Preparing build 03-Feb-2017 16:22:50 e24a372680fc: Preparing build 03-Feb-2017 16:22:50 5eb5bd4c5014: Preparing build 03-Feb-2017 16:22:50 d195a7a18c70: Preparing build 03-Feb-2017 16:22:50 af605e724c5a: Preparing build 03-Feb-2017 16:22:50 59f161c3069d: Preparing build 03-Feb-2017 16:22:50 4f03495a4d7d: Preparing build 03-Feb-2017 16:22:50 7d760664bbad: Waiting build 03-Feb-2017 16:22:50 a2688f6622a7: Waiting build 03-Feb-2017 16:22:50 e24a372680fc: Waiting build 03-Feb-2017 16:22:50 5eb5bd4c5014: Waiting build 03-Feb-2017 16:22:50 d195a7a18c70: Waiting build 03-Feb-2017 16:22:50 af605e724c5a: Waiting build 03-Feb-2017 16:22:50 59f161c3069d: Waiting build 03-Feb-2017 16:22:50 4f03495a4d7d: Waiting build 03-Feb-2017 16:22:50 dce1077ded56: Layer already exists build 03-Feb-2017 16:22:50 a3a514ba80a3: Layer already exists build 03-Feb-2017 16:22:50 bfc8a6a4f87c: Layer already exists build 03-Feb-2017 16:22:50 a31423c85135: Layer already exists build 03-Feb-2017 16:22:50 5e269aa11a2f: Layer already exists build 03-Feb-2017 16:22:50 7d760664bbad: Layer already exists build 03-Feb-2017 16:22:50 a2688f6622a7: Layer already exists build 03-Feb-2017 16:22:51 e24a372680fc: Layer already exists build 03-Feb-2017 16:22:51 5eb5bd4c5014: Layer already exists build 03-Feb-2017 16:22:51 d195a7a18c70: Layer already exists build 03-Feb-2017 16:22:51 4f03495a4d7d: Layer already exists build 03-Feb-2017 16:22:51 af605e724c5a: Layer already exists build 03-Feb-2017 16:22:51 59f161c3069d: Layer already exists build 03-Feb-2017 16:22:51 latest: digest: sha256:d6824ae03568dc8e5aa5d2d6ed336c51556b632d695e60f8c14a31ab1f5324a7 size: 3031 build 03-Feb-2017 16:22:51 Untagged: 23804:latest build 03-Feb-2017 16:22:51 Sending build context to Docker daemon 66.05 kB build 03-Feb-2017 16:22:51 build 03-Feb-2017 16:22:51 Step 1 : FROM clowder/pyclowder:1 build 03-Feb-2017 16:22:51 ---> 2dd17798784b build 03-Feb-2017 16:22:51 Step 2 : MAINTAINER Yan Zhao build 03-Feb-2017 16:22:51 ---> Using cache build 03-Feb-2017 16:22:51 ---> 2c58a262fb36 build 03-Feb-2017 16:22:51 Step 3 : 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 03-Feb-2017 16:22:51 ---> Running in 26036dddeec4 build 03-Feb-2017 16:22:51 ---> edde6fffd087 build 03-Feb-2017 16:22:51 Removing intermediate container 26036dddeec4 build 03-Feb-2017 16:22:51 Step 4 : USER root build 03-Feb-2017 16:22:51 ---> Running in 1824827bdbe1 build 03-Feb-2017 16:22:52 ---> 532e959b4b25 build 03-Feb-2017 16:22:52 Removing intermediate container 1824827bdbe1 build 03-Feb-2017 16:22:52 Step 5 : COPY requirements.txt /home/clowder/ build 03-Feb-2017 16:22:52 ---> 8530a774b16e build 03-Feb-2017 16:22:52 Removing intermediate container 2a036a9dfe6c build 03-Feb-2017 16:22:52 Step 6 : RUN pip install --upgrade pip build 03-Feb-2017 16:22:52 ---> Running in b52ad4fd4292 build 03-Feb-2017 16:22:54 Collecting pip build 03-Feb-2017 16:22:54 Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB) build 03-Feb-2017 16:22:55 Installing collected packages: pip build 03-Feb-2017 16:22:55 Found existing installation: pip 8.1.1 build 03-Feb-2017 16:22:55 Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr build 03-Feb-2017 16:22:56 Successfully installed pip-9.0.1 build 03-Feb-2017 16:22:57 ---> cbc6f4673288 build 03-Feb-2017 16:22:57 Removing intermediate container b52ad4fd4292 build 03-Feb-2017 16:22:57 Step 7 : RUN pip install -r /home/clowder/requirements.txt build 03-Feb-2017 16:22:57 ---> Running in 7afcf8091021 build 03-Feb-2017 16:22:58 Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) build 03-Feb-2017 16:22:58 Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2)) build 03-Feb-2017 16:22:58 Downloading openpyxl-1.6.2.tar.gz (199kB) build 03-Feb-2017 16:22:59 Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3)) build 03-Feb-2017 16:22:59 Downloading pika-0.9.14.tar.gz (72kB) build 03-Feb-2017 16:23:00 Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4)) build 03-Feb-2017 16:23:01 Downloading pymongo-3.2.1.tar.gz (647kB) build 03-Feb-2017 16:23:02 Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5)) build 03-Feb-2017 16:23:02 Downloading pytz-2014.3.zip (482kB) build 03-Feb-2017 16:23:03 Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6)) build 03-Feb-2017 16:23:03 Downloading requests-2.2.1-py2.py3-none-any.whl (625kB) build 03-Feb-2017 16:23:03 Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) build 03-Feb-2017 16:23:03 Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8)) build 03-Feb-2017 16:23:04 Downloading xlrd-0.9.3.tar.gz (178kB) build 03-Feb-2017 16:23:04 Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd build 03-Feb-2017 16:23:04 Running setup.py install for openpyxl: started build 03-Feb-2017 16:23:05 Running setup.py install for openpyxl: finished with status 'done' build 03-Feb-2017 16:23:05 Found existing installation: pika 0.10.0 build 03-Feb-2017 16:23:05 Uninstalling pika-0.10.0: build 03-Feb-2017 16:23:05 Successfully uninstalled pika-0.10.0 build 03-Feb-2017 16:23:05 Running setup.py install for pika: started build 03-Feb-2017 16:23:05 Running setup.py install for pika: finished with status 'done' build 03-Feb-2017 16:23:05 Running setup.py install for pymongo: started build 03-Feb-2017 16:23:06 Running setup.py install for pymongo: finished with status 'done' build 03-Feb-2017 16:23:06 Running setup.py install for pytz: started build 03-Feb-2017 16:23:06 Running setup.py install for pytz: finished with status 'done' build 03-Feb-2017 16:23:07 Found existing installation: requests 2.13.0 build 03-Feb-2017 16:23:07 Uninstalling requests-2.13.0: build 03-Feb-2017 16:23:07 Successfully uninstalled requests-2.13.0 build 03-Feb-2017 16:23:07 Running setup.py install for xlrd: started build 03-Feb-2017 16:23:08 Running setup.py install for xlrd: finished with status 'done' build 03-Feb-2017 16:23:08 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 03-Feb-2017 16:23:09 ---> e5278fd0c8f4 build 03-Feb-2017 16:23:09 Removing intermediate container 7afcf8091021 build 03-Feb-2017 16:23:09 Step 8 : USER clowder build 03-Feb-2017 16:23:09 ---> Running in 5a72627b9aa3 build 03-Feb-2017 16:23:09 ---> cf400c216594 build 03-Feb-2017 16:23:09 Removing intermediate container 5a72627b9aa3 build 03-Feb-2017 16:23:09 Step 9 : COPY entrypoint.sh *.py *.json /home/clowder/ build 03-Feb-2017 16:23:10 ---> 33d7e2db3fb3 build 03-Feb-2017 16:23:10 Removing intermediate container 79d72e1b8966 build 03-Feb-2017 16:23:10 Step 10 : ENTRYPOINT /home/clowder/entrypoint.sh build 03-Feb-2017 16:23:10 ---> Running in 730e7e5db9b1 build 03-Feb-2017 16:23:10 ---> a559a8146b12 build 03-Feb-2017 16:23:10 Removing intermediate container 730e7e5db9b1 build 03-Feb-2017 16:23:10 Step 11 : CMD extractor build 03-Feb-2017 16:23:10 ---> Running in 6e87f09da454 build 03-Feb-2017 16:23:10 ---> 4645f1bdd0a5 build 03-Feb-2017 16:23:10 Removing intermediate container 6e87f09da454 build 03-Feb-2017 16:23:10 Successfully built 4645f1bdd0a5 build 03-Feb-2017 16:23:10 The push refers to a repository [docker.io/clowder/extractors-msc-chemcbc] build 03-Feb-2017 16:23:10 c21ee9275513: Preparing build 03-Feb-2017 16:23:10 1ecac42e291e: Preparing build 03-Feb-2017 16:23:10 07139b34af0e: Preparing build 03-Feb-2017 16:23:10 ae7edbcc83c8: Preparing build 03-Feb-2017 16:23:10 5e269aa11a2f: Preparing build 03-Feb-2017 16:23:10 7d760664bbad: Preparing build 03-Feb-2017 16:23:10 a2688f6622a7: Preparing build 03-Feb-2017 16:23:10 e24a372680fc: Preparing build 03-Feb-2017 16:23:10 5eb5bd4c5014: Preparing build 03-Feb-2017 16:23:10 d195a7a18c70: Preparing build 03-Feb-2017 16:23:10 af605e724c5a: Preparing build 03-Feb-2017 16:23:10 59f161c3069d: Preparing build 03-Feb-2017 16:23:10 4f03495a4d7d: Preparing build 03-Feb-2017 16:23:10 7d760664bbad: Waiting build 03-Feb-2017 16:23:10 a2688f6622a7: Waiting build 03-Feb-2017 16:23:10 af605e724c5a: Waiting build 03-Feb-2017 16:23:10 e24a372680fc: Waiting build 03-Feb-2017 16:23:10 5eb5bd4c5014: Waiting build 03-Feb-2017 16:23:10 d195a7a18c70: Waiting build 03-Feb-2017 16:23:10 59f161c3069d: Waiting build 03-Feb-2017 16:23:10 4f03495a4d7d: Waiting build 03-Feb-2017 16:23:11 5e269aa11a2f: Mounted from clowder/extractors-msc-islet build 03-Feb-2017 16:23:12 7d760664bbad: Mounted from clowder/extractors-msc-islet build 03-Feb-2017 16:23:13 a2688f6622a7: Mounted from clowder/extractors-msc-islet build 03-Feb-2017 16:23:13 ae7edbcc83c8: Pushed build 03-Feb-2017 16:23:13 e24a372680fc: Mounted from clowder/extractors-msc-islet build 03-Feb-2017 16:23:13 c21ee9275513: Pushed build 03-Feb-2017 16:23:14 5eb5bd4c5014: Mounted from clowder/extractors-msc-islet build 03-Feb-2017 16:23:14 af605e724c5a: Mounted from clowder/extractors-msc-islet build 03-Feb-2017 16:23:14 d195a7a18c70: Mounted from clowder/extractors-msc-islet build 03-Feb-2017 16:23:14 4f03495a4d7d: Mounted from clowder/extractors-msc-islet build 03-Feb-2017 16:23:14 59f161c3069d: Mounted from clowder/extractors-msc-islet build 03-Feb-2017 16:23:14 07139b34af0e: Pushed build 03-Feb-2017 16:23:14 1ecac42e291e: Pushed build 03-Feb-2017 16:23:17 master: digest: sha256:14262b69263819dcfd8f01f705a6c19a6c265c09016d1de73778b193096c83be size: 3031 build 03-Feb-2017 16:23:17 The push refers to a repository [docker.io/clowder/extractors-msc-chemcbc] build 03-Feb-2017 16:23:17 c21ee9275513: Preparing build 03-Feb-2017 16:23:17 1ecac42e291e: Preparing build 03-Feb-2017 16:23:17 07139b34af0e: Preparing build 03-Feb-2017 16:23:17 ae7edbcc83c8: Preparing build 03-Feb-2017 16:23:17 5e269aa11a2f: Preparing build 03-Feb-2017 16:23:17 7d760664bbad: Preparing build 03-Feb-2017 16:23:17 a2688f6622a7: Preparing build 03-Feb-2017 16:23:17 e24a372680fc: Preparing build 03-Feb-2017 16:23:17 5eb5bd4c5014: Preparing build 03-Feb-2017 16:23:17 d195a7a18c70: Preparing build 03-Feb-2017 16:23:17 af605e724c5a: Preparing build 03-Feb-2017 16:23:17 59f161c3069d: Preparing build 03-Feb-2017 16:23:17 4f03495a4d7d: Preparing build 03-Feb-2017 16:23:17 7d760664bbad: Waiting build 03-Feb-2017 16:23:17 a2688f6622a7: Waiting build 03-Feb-2017 16:23:17 e24a372680fc: Waiting build 03-Feb-2017 16:23:17 d195a7a18c70: Waiting build 03-Feb-2017 16:23:17 af605e724c5a: Waiting build 03-Feb-2017 16:23:17 59f161c3069d: Waiting build 03-Feb-2017 16:23:17 5eb5bd4c5014: Waiting build 03-Feb-2017 16:23:17 4f03495a4d7d: Waiting build 03-Feb-2017 16:23:18 07139b34af0e: Layer already exists build 03-Feb-2017 16:23:18 5e269aa11a2f: Layer already exists build 03-Feb-2017 16:23:18 ae7edbcc83c8: Layer already exists build 03-Feb-2017 16:23:18 c21ee9275513: Layer already exists build 03-Feb-2017 16:23:18 1ecac42e291e: Layer already exists build 03-Feb-2017 16:23:18 e24a372680fc: Layer already exists build 03-Feb-2017 16:23:18 a2688f6622a7: Layer already exists build 03-Feb-2017 16:23:18 5eb5bd4c5014: Layer already exists build 03-Feb-2017 16:23:18 7d760664bbad: Layer already exists build 03-Feb-2017 16:23:18 d195a7a18c70: Layer already exists build 03-Feb-2017 16:23:18 4f03495a4d7d: Layer already exists build 03-Feb-2017 16:23:18 af605e724c5a: Layer already exists build 03-Feb-2017 16:23:18 59f161c3069d: Layer already exists build 03-Feb-2017 16:23:19 latest: digest: sha256:14262b69263819dcfd8f01f705a6c19a6c265c09016d1de73778b193096c83be size: 3031 build 03-Feb-2017 16:23:19 Untagged: 23804:latest build 03-Feb-2017 16:23:19 Sending build context to Docker daemon 198.1 kB build 03-Feb-2017 16:23:19 build 03-Feb-2017 16:23:19 Step 1 : FROM clowder/pyclowder:1 build 03-Feb-2017 16:23:19 ---> 2dd17798784b build 03-Feb-2017 16:23:19 Step 2 : MAINTAINER Yan Zhao build 03-Feb-2017 16:23:19 ---> Using cache build 03-Feb-2017 16:23:19 ---> 2c58a262fb36 build 03-Feb-2017 16:23:19 Step 3 : 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 03-Feb-2017 16:23:19 ---> Running in 7f2286eeac76 build 03-Feb-2017 16:23:19 ---> c15e5992493d build 03-Feb-2017 16:23:19 Removing intermediate container 7f2286eeac76 build 03-Feb-2017 16:23:19 Step 4 : USER root build 03-Feb-2017 16:23:19 ---> Running in ce38ba90307f build 03-Feb-2017 16:23:19 ---> cfa406d63bb4 build 03-Feb-2017 16:23:19 Removing intermediate container ce38ba90307f build 03-Feb-2017 16:23:19 Step 5 : COPY requirements.txt /home/clowder/ build 03-Feb-2017 16:23:19 ---> e133d968fbac build 03-Feb-2017 16:23:19 Removing intermediate container 571ca394d872 build 03-Feb-2017 16:23:19 Step 6 : RUN pip install --upgrade pip build 03-Feb-2017 16:23:19 ---> Running in 5e5a9d8b9a3d build 03-Feb-2017 16:23:21 Collecting pip build 03-Feb-2017 16:23:21 Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB) build 03-Feb-2017 16:23:21 Installing collected packages: pip build 03-Feb-2017 16:23:21 Found existing installation: pip 8.1.1 build 03-Feb-2017 16:23:21 Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr build 03-Feb-2017 16:23:23 Successfully installed pip-9.0.1 build 03-Feb-2017 16:23:24 ---> 513371ef8839 build 03-Feb-2017 16:23:24 Removing intermediate container 5e5a9d8b9a3d build 03-Feb-2017 16:23:24 Step 7 : RUN pip install -r /home/clowder/requirements.txt build 03-Feb-2017 16:23:24 ---> Running in 5cb01f3d98d3 build 03-Feb-2017 16:23:25 Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) build 03-Feb-2017 16:23:25 Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2)) build 03-Feb-2017 16:23:25 Downloading openpyxl-1.6.2.tar.gz (199kB) build 03-Feb-2017 16:23:26 Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3)) build 03-Feb-2017 16:23:26 Downloading pika-0.9.14.tar.gz (72kB) build 03-Feb-2017 16:23:27 Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4)) build 03-Feb-2017 16:23:28 Downloading pymongo-3.2.1.tar.gz (647kB) build 03-Feb-2017 16:23:29 Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5)) build 03-Feb-2017 16:23:29 Downloading pytz-2014.3.zip (482kB) build 03-Feb-2017 16:23:30 Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6)) build 03-Feb-2017 16:23:30 Downloading requests-2.2.1-py2.py3-none-any.whl (625kB) build 03-Feb-2017 16:23:30 Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) build 03-Feb-2017 16:23:30 Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8)) build 03-Feb-2017 16:23:30 Downloading xlrd-0.9.3.tar.gz (178kB) build 03-Feb-2017 16:23:31 Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd build 03-Feb-2017 16:23:31 Running setup.py install for openpyxl: started build 03-Feb-2017 16:23:32 Running setup.py install for openpyxl: finished with status 'done' build 03-Feb-2017 16:23:32 Found existing installation: pika 0.10.0 build 03-Feb-2017 16:23:32 Uninstalling pika-0.10.0: build 03-Feb-2017 16:23:32 Successfully uninstalled pika-0.10.0 build 03-Feb-2017 16:23:32 Running setup.py install for pika: started build 03-Feb-2017 16:23:32 Running setup.py install for pika: finished with status 'done' build 03-Feb-2017 16:23:32 Running setup.py install for pymongo: started build 03-Feb-2017 16:23:33 Running setup.py install for pymongo: finished with status 'done' build 03-Feb-2017 16:23:33 Running setup.py install for pytz: started build 03-Feb-2017 16:23:35 Running setup.py install for pytz: finished with status 'done' build 03-Feb-2017 16:23:35 Found existing installation: requests 2.13.0 build 03-Feb-2017 16:23:35 Uninstalling requests-2.13.0: build 03-Feb-2017 16:23:35 Successfully uninstalled requests-2.13.0 build 03-Feb-2017 16:23:36 Running setup.py install for xlrd: started build 03-Feb-2017 16:23:37 Running setup.py install for xlrd: finished with status 'done' build 03-Feb-2017 16:23:37 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 03-Feb-2017 16:23:38 ---> 1639935ea97b build 03-Feb-2017 16:23:38 Removing intermediate container 5cb01f3d98d3 build 03-Feb-2017 16:23:38 Step 8 : USER clowder build 03-Feb-2017 16:23:38 ---> Running in 4b818bc97c6f build 03-Feb-2017 16:23:38 ---> b8debf14c9c5 build 03-Feb-2017 16:23:38 Removing intermediate container 4b818bc97c6f build 03-Feb-2017 16:23:38 Step 9 : COPY entrypoint.sh *.py *.json /home/clowder/ build 03-Feb-2017 16:23:39 ---> 4d394e498c64 build 03-Feb-2017 16:23:39 Removing intermediate container 3dda94a590c2 build 03-Feb-2017 16:23:39 Step 10 : ENTRYPOINT /home/clowder/entrypoint.sh build 03-Feb-2017 16:23:39 ---> Running in 7ca2cd50ccc1 build 03-Feb-2017 16:23:39 ---> 39faf5180305 build 03-Feb-2017 16:23:39 Removing intermediate container 7ca2cd50ccc1 build 03-Feb-2017 16:23:39 Step 11 : CMD extractor build 03-Feb-2017 16:23:39 ---> Running in 697be9085928 build 03-Feb-2017 16:23:40 ---> cec07945682a build 03-Feb-2017 16:23:40 Removing intermediate container 697be9085928 build 03-Feb-2017 16:23:40 Successfully built cec07945682a build 03-Feb-2017 16:23:40 The push refers to a repository [docker.io/clowder/extractors-msc-monitor] build 03-Feb-2017 16:23:40 c940dde0cb97: Preparing build 03-Feb-2017 16:23:40 2708bbab64b3: Preparing build 03-Feb-2017 16:23:40 4deb76aa51e5: Preparing build 03-Feb-2017 16:23:40 a19440beedca: Preparing build 03-Feb-2017 16:23:40 5e269aa11a2f: Preparing build 03-Feb-2017 16:23:40 7d760664bbad: Preparing build 03-Feb-2017 16:23:40 a2688f6622a7: Preparing build 03-Feb-2017 16:23:40 e24a372680fc: Preparing build 03-Feb-2017 16:23:40 5eb5bd4c5014: Preparing build 03-Feb-2017 16:23:40 7d760664bbad: Waiting build 03-Feb-2017 16:23:40 d195a7a18c70: Preparing build 03-Feb-2017 16:23:40 af605e724c5a: Preparing build 03-Feb-2017 16:23:40 59f161c3069d: Preparing build 03-Feb-2017 16:23:40 4f03495a4d7d: Preparing build 03-Feb-2017 16:23:40 a2688f6622a7: Waiting build 03-Feb-2017 16:23:40 e24a372680fc: Waiting build 03-Feb-2017 16:23:40 5eb5bd4c5014: Waiting build 03-Feb-2017 16:23:40 d195a7a18c70: Waiting build 03-Feb-2017 16:23:40 af605e724c5a: Waiting build 03-Feb-2017 16:23:40 59f161c3069d: Waiting build 03-Feb-2017 16:23:40 4f03495a4d7d: Waiting build 03-Feb-2017 16:23:41 5e269aa11a2f: Mounted from clowder/extractors-msc-chemcbc build 03-Feb-2017 16:23:42 7d760664bbad: Mounted from clowder/extractors-msc-chemcbc build 03-Feb-2017 16:23:42 c940dde0cb97: Pushed build 03-Feb-2017 16:23:42 a19440beedca: Pushed build 03-Feb-2017 16:23:42 a2688f6622a7: Mounted from clowder/extractors-msc-chemcbc build 03-Feb-2017 16:23:42 e24a372680fc: Mounted from clowder/extractors-msc-chemcbc build 03-Feb-2017 16:23:43 5eb5bd4c5014: Mounted from clowder/extractors-msc-chemcbc build 03-Feb-2017 16:23:43 af605e724c5a: Mounted from clowder/extractors-msc-chemcbc build 03-Feb-2017 16:23:43 d195a7a18c70: Mounted from clowder/extractors-msc-chemcbc build 03-Feb-2017 16:23:43 59f161c3069d: Mounted from clowder/extractors-msc-chemcbc build 03-Feb-2017 16:23:43 4deb76aa51e5: Pushed build 03-Feb-2017 16:23:44 4f03495a4d7d: Mounted from clowder/extractors-msc-chemcbc build 03-Feb-2017 16:23:45 2708bbab64b3: Pushed build 03-Feb-2017 16:23:48 master: digest: sha256:953fc17951608a54f931199cb77f6c65ace872740527d7e2ee2c6f86f8ccf989 size: 3031 build 03-Feb-2017 16:23:48 The push refers to a repository [docker.io/clowder/extractors-msc-monitor] build 03-Feb-2017 16:23:48 c940dde0cb97: Preparing build 03-Feb-2017 16:23:48 2708bbab64b3: Preparing build 03-Feb-2017 16:23:48 4deb76aa51e5: Preparing build 03-Feb-2017 16:23:48 a19440beedca: Preparing build 03-Feb-2017 16:23:48 5e269aa11a2f: Preparing build 03-Feb-2017 16:23:48 7d760664bbad: Preparing build 03-Feb-2017 16:23:48 a2688f6622a7: Preparing build 03-Feb-2017 16:23:48 e24a372680fc: Preparing build 03-Feb-2017 16:23:48 5eb5bd4c5014: Preparing build 03-Feb-2017 16:23:48 d195a7a18c70: Preparing build 03-Feb-2017 16:23:48 af605e724c5a: Preparing build 03-Feb-2017 16:23:48 59f161c3069d: Preparing build 03-Feb-2017 16:23:48 4f03495a4d7d: Preparing build 03-Feb-2017 16:23:48 e24a372680fc: Waiting build 03-Feb-2017 16:23:48 5eb5bd4c5014: Waiting build 03-Feb-2017 16:23:48 d195a7a18c70: Waiting build 03-Feb-2017 16:23:48 af605e724c5a: Waiting build 03-Feb-2017 16:23:48 59f161c3069d: Waiting build 03-Feb-2017 16:23:48 4f03495a4d7d: Waiting build 03-Feb-2017 16:23:48 7d760664bbad: Waiting build 03-Feb-2017 16:23:48 a2688f6622a7: Waiting build 03-Feb-2017 16:23:49 a19440beedca: Layer already exists build 03-Feb-2017 16:23:49 c940dde0cb97: Layer already exists build 03-Feb-2017 16:23:49 5e269aa11a2f: Layer already exists build 03-Feb-2017 16:23:49 2708bbab64b3: Layer already exists build 03-Feb-2017 16:23:49 4deb76aa51e5: Layer already exists build 03-Feb-2017 16:23:49 7d760664bbad: Layer already exists build 03-Feb-2017 16:23:49 e24a372680fc: Layer already exists build 03-Feb-2017 16:23:49 a2688f6622a7: Layer already exists build 03-Feb-2017 16:23:49 5eb5bd4c5014: Layer already exists build 03-Feb-2017 16:23:49 d195a7a18c70: Layer already exists build 03-Feb-2017 16:23:49 af605e724c5a: Layer already exists build 03-Feb-2017 16:23:49 4f03495a4d7d: Layer already exists build 03-Feb-2017 16:23:49 59f161c3069d: Layer already exists build 03-Feb-2017 16:23:49 latest: digest: sha256:953fc17951608a54f931199cb77f6c65ace872740527d7e2ee2c6f86f8ccf989 size: 3031 build 03-Feb-2017 16:23:49 Untagged: 23804:latest build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 557.1 kB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 1.114 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 1.671 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 2.228 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 2.785 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 3.342 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 3.899 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 4.456 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 5.014 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 5.571 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 6.128 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 6.685 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 7.242 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 7.799 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 8.356 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 8.913 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 9.47 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 10.03 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 10.58 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 11.14 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 11.7 MB build 03-Feb-2017 16:23:50 Sending build context to Docker daemon 12.1 MB build 03-Feb-2017 16:23:50 build 03-Feb-2017 16:23:50 Step 1 : FROM clowder/pyclowder:1 build 03-Feb-2017 16:23:50 ---> 2dd17798784b build 03-Feb-2017 16:23:50 Step 2 : MAINTAINER Yan Zhao build 03-Feb-2017 16:23:50 ---> Using cache build 03-Feb-2017 16:23:50 ---> 2c58a262fb36 build 03-Feb-2017 16:23:50 Step 3 : 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 03-Feb-2017 16:23:50 ---> Running in 82e10ee52b08 build 03-Feb-2017 16:23:50 ---> 7c7ba4ec74c5 build 03-Feb-2017 16:23:50 Removing intermediate container 82e10ee52b08 build 03-Feb-2017 16:23:50 Step 4 : USER root build 03-Feb-2017 16:23:50 ---> Running in 793dc91b04b2 build 03-Feb-2017 16:23:50 ---> 4012d5c13d3a build 03-Feb-2017 16:23:50 Removing intermediate container 793dc91b04b2 build 03-Feb-2017 16:23:50 Step 5 : COPY requirements.txt /home/clowder/ build 03-Feb-2017 16:23:50 ---> bd9372224242 build 03-Feb-2017 16:23:50 Removing intermediate container c7b1be05b56c build 03-Feb-2017 16:23:50 Step 6 : RUN pip install --upgrade pip build 03-Feb-2017 16:23:50 ---> Running in 22eefddd9d38 build 03-Feb-2017 16:23:52 Collecting pip build 03-Feb-2017 16:23:52 Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB) build 03-Feb-2017 16:23:53 Installing collected packages: pip build 03-Feb-2017 16:23:53 Found existing installation: pip 8.1.1 build 03-Feb-2017 16:23:53 Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr build 03-Feb-2017 16:23:54 Successfully installed pip-9.0.1 build 03-Feb-2017 16:23:54 ---> 47a63a76bfde build 03-Feb-2017 16:23:54 Removing intermediate container 22eefddd9d38 build 03-Feb-2017 16:23:54 Step 7 : RUN pip install -r /home/clowder/requirements.txt build 03-Feb-2017 16:23:55 ---> Running in c668c94d9d56 build 03-Feb-2017 16:23:55 Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) build 03-Feb-2017 16:23:56 Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2)) build 03-Feb-2017 16:23:56 Downloading openpyxl-1.6.2.tar.gz (199kB) build 03-Feb-2017 16:23:57 Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3)) build 03-Feb-2017 16:23:57 Downloading pika-0.9.14.tar.gz (72kB) build 03-Feb-2017 16:23:57 Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4)) build 03-Feb-2017 16:23:58 Downloading pymongo-3.2.1.tar.gz (647kB) build 03-Feb-2017 16:23:59 Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5)) build 03-Feb-2017 16:23:59 Downloading pytz-2014.3.zip (482kB) build 03-Feb-2017 16:24:00 Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6)) build 03-Feb-2017 16:24:01 Downloading requests-2.2.1-py2.py3-none-any.whl (625kB) build 03-Feb-2017 16:24:01 Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) build 03-Feb-2017 16:24:01 Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8)) build 03-Feb-2017 16:24:01 Downloading xlrd-0.9.3.tar.gz (178kB) build 03-Feb-2017 16:24:02 Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd build 03-Feb-2017 16:24:02 Running setup.py install for openpyxl: started build 03-Feb-2017 16:24:02 Running setup.py install for openpyxl: finished with status 'done' build 03-Feb-2017 16:24:03 Found existing installation: pika 0.10.0 build 03-Feb-2017 16:24:03 Uninstalling pika-0.10.0: build 03-Feb-2017 16:24:03 Successfully uninstalled pika-0.10.0 build 03-Feb-2017 16:24:03 Running setup.py install for pika: started build 03-Feb-2017 16:24:03 Running setup.py install for pika: finished with status 'done' build 03-Feb-2017 16:24:03 Running setup.py install for pymongo: started build 03-Feb-2017 16:24:03 Running setup.py install for pymongo: finished with status 'done' build 03-Feb-2017 16:24:04 Running setup.py install for pytz: started build 03-Feb-2017 16:24:04 Running setup.py install for pytz: finished with status 'done' build 03-Feb-2017 16:24:04 Found existing installation: requests 2.13.0 build 03-Feb-2017 16:24:04 Uninstalling requests-2.13.0: build 03-Feb-2017 16:24:05 Successfully uninstalled requests-2.13.0 build 03-Feb-2017 16:24:05 Running setup.py install for xlrd: started build 03-Feb-2017 16:24:06 Running setup.py install for xlrd: finished with status 'done' build 03-Feb-2017 16:24:06 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 03-Feb-2017 16:24:07 ---> fc64f47646c2 build 03-Feb-2017 16:24:07 Removing intermediate container c668c94d9d56 build 03-Feb-2017 16:24:07 Step 8 : USER clowder build 03-Feb-2017 16:24:07 ---> Running in 12f6bed617f4 build 03-Feb-2017 16:24:07 ---> bf28b5f50168 build 03-Feb-2017 16:24:07 Removing intermediate container 12f6bed617f4 build 03-Feb-2017 16:24:07 Step 9 : COPY entrypoint.sh *.py *.json /home/clowder/ build 03-Feb-2017 16:24:07 ---> c420a8202720 build 03-Feb-2017 16:24:07 Removing intermediate container b4b32c85780d build 03-Feb-2017 16:24:07 Step 10 : ENTRYPOINT /home/clowder/entrypoint.sh build 03-Feb-2017 16:24:08 ---> Running in d2d2d16cfa09 build 03-Feb-2017 16:24:08 ---> 49510b15f297 build 03-Feb-2017 16:24:08 Removing intermediate container d2d2d16cfa09 build 03-Feb-2017 16:24:08 Step 11 : CMD extractor build 03-Feb-2017 16:24:08 ---> Running in 3e0fede85eff build 03-Feb-2017 16:24:08 ---> 44cf7749aa77 build 03-Feb-2017 16:24:08 Removing intermediate container 3e0fede85eff build 03-Feb-2017 16:24:08 Successfully built 44cf7749aa77 build 03-Feb-2017 16:24:08 The push refers to a repository [docker.io/clowder/extractors-msc-phenotype] build 03-Feb-2017 16:24:08 0b9105b5841e: Preparing build 03-Feb-2017 16:24:08 df7c68aadd5c: Preparing build 03-Feb-2017 16:24:08 f6520917d756: Preparing build 03-Feb-2017 16:24:08 fc5535cc0a1e: Preparing build 03-Feb-2017 16:24:08 5e269aa11a2f: Preparing build 03-Feb-2017 16:24:08 7d760664bbad: Preparing build 03-Feb-2017 16:24:08 a2688f6622a7: Preparing build 03-Feb-2017 16:24:08 e24a372680fc: Preparing build 03-Feb-2017 16:24:08 5eb5bd4c5014: Preparing build 03-Feb-2017 16:24:08 d195a7a18c70: Preparing build 03-Feb-2017 16:24:08 af605e724c5a: Preparing build 03-Feb-2017 16:24:08 59f161c3069d: Preparing build 03-Feb-2017 16:24:08 4f03495a4d7d: Preparing build 03-Feb-2017 16:24:08 7d760664bbad: Waiting build 03-Feb-2017 16:24:08 a2688f6622a7: Waiting build 03-Feb-2017 16:24:08 e24a372680fc: Waiting build 03-Feb-2017 16:24:08 5eb5bd4c5014: Waiting build 03-Feb-2017 16:24:08 d195a7a18c70: Waiting build 03-Feb-2017 16:24:08 59f161c3069d: Waiting build 03-Feb-2017 16:24:08 4f03495a4d7d: Waiting build 03-Feb-2017 16:24:08 af605e724c5a: Waiting build 03-Feb-2017 16:24:09 5e269aa11a2f: Mounted from clowder/extractors-msc-monitor build 03-Feb-2017 16:24:10 7d760664bbad: Mounted from clowder/extractors-msc-monitor build 03-Feb-2017 16:24:11 0b9105b5841e: Pushed build 03-Feb-2017 16:24:11 fc5535cc0a1e: Pushed build 03-Feb-2017 16:24:11 a2688f6622a7: Mounted from clowder/extractors-msc-monitor build 03-Feb-2017 16:24:11 e24a372680fc: Mounted from clowder/extractors-msc-monitor build 03-Feb-2017 16:24:11 5eb5bd4c5014: Mounted from clowder/extractors-msc-monitor build 03-Feb-2017 16:24:11 d195a7a18c70: Mounted from clowder/extractors-msc-monitor build 03-Feb-2017 16:24:12 af605e724c5a: Mounted from clowder/extractors-msc-monitor build 03-Feb-2017 16:24:12 59f161c3069d: Mounted from clowder/extractors-msc-monitor build 03-Feb-2017 16:24:12 4f03495a4d7d: Mounted from clowder/extractors-msc-monitor build 03-Feb-2017 16:24:12 f6520917d756: Pushed build 03-Feb-2017 16:24:13 df7c68aadd5c: Pushed build 03-Feb-2017 16:24:15 master: digest: sha256:0e81355fdf6cd7082cb829bb9ccca289c79d58d3c07388ee0664c75d6e6a95ae size: 3031 build 03-Feb-2017 16:24:16 The push refers to a repository [docker.io/clowder/extractors-msc-phenotype] build 03-Feb-2017 16:24:16 0b9105b5841e: Preparing build 03-Feb-2017 16:24:16 df7c68aadd5c: Preparing build 03-Feb-2017 16:24:16 f6520917d756: Preparing build 03-Feb-2017 16:24:16 fc5535cc0a1e: Preparing build 03-Feb-2017 16:24:16 5e269aa11a2f: Preparing build 03-Feb-2017 16:24:16 7d760664bbad: Preparing build 03-Feb-2017 16:24:16 a2688f6622a7: Preparing build 03-Feb-2017 16:24:16 e24a372680fc: Preparing build 03-Feb-2017 16:24:16 5eb5bd4c5014: Preparing build 03-Feb-2017 16:24:16 d195a7a18c70: Preparing build 03-Feb-2017 16:24:16 af605e724c5a: Preparing build 03-Feb-2017 16:24:16 59f161c3069d: Preparing build 03-Feb-2017 16:24:16 4f03495a4d7d: Preparing build 03-Feb-2017 16:24:16 5eb5bd4c5014: Waiting build 03-Feb-2017 16:24:16 d195a7a18c70: Waiting build 03-Feb-2017 16:24:16 af605e724c5a: Waiting build 03-Feb-2017 16:24:16 59f161c3069d: Waiting build 03-Feb-2017 16:24:16 4f03495a4d7d: Waiting build 03-Feb-2017 16:24:16 7d760664bbad: Waiting build 03-Feb-2017 16:24:16 a2688f6622a7: Waiting build 03-Feb-2017 16:24:16 e24a372680fc: Waiting build 03-Feb-2017 16:24:16 f6520917d756: Layer already exists build 03-Feb-2017 16:24:16 df7c68aadd5c: Layer already exists build 03-Feb-2017 16:24:16 fc5535cc0a1e: Layer already exists build 03-Feb-2017 16:24:16 5e269aa11a2f: Layer already exists build 03-Feb-2017 16:24:16 0b9105b5841e: Layer already exists build 03-Feb-2017 16:24:16 7d760664bbad: Layer already exists build 03-Feb-2017 16:24:16 e24a372680fc: Layer already exists build 03-Feb-2017 16:24:16 d195a7a18c70: Layer already exists build 03-Feb-2017 16:24:16 5eb5bd4c5014: Layer already exists build 03-Feb-2017 16:24:16 a2688f6622a7: Layer already exists build 03-Feb-2017 16:24:16 af605e724c5a: Layer already exists build 03-Feb-2017 16:24:16 59f161c3069d: Layer already exists build 03-Feb-2017 16:24:17 4f03495a4d7d: Layer already exists build 03-Feb-2017 16:24:17 latest: digest: sha256:0e81355fdf6cd7082cb829bb9ccca289c79d58d3c07388ee0664c75d6e6a95ae size: 3031 build 03-Feb-2017 16:24:17 Untagged: 23804:latest simple 03-Feb-2017 16:24:17 Finished task 'docker build' with result: Success simple 03-Feb-2017 16:24:17 Running post build plugin 'Docker Container Cleanup' simple 03-Feb-2017 16:24:18 Running post build plugin 'NCover Results Collector' simple 03-Feb-2017 16:24:18 Running post build plugin 'Clover Results Collector' simple 03-Feb-2017 16:24:18 Running post build plugin 'npm Cache Cleanup' simple 03-Feb-2017 16:24:18 Running post build plugin 'Artifact Copier' simple 03-Feb-2017 16:24:18 Finalising the build... simple 03-Feb-2017 16:24:18 Stopping timer. simple 03-Feb-2017 16:24:18 Build CATS-MSC1-JOB1-2 completed. simple 03-Feb-2017 16:24:18 Running on server: post build plugin 'NCover Results Collector' simple 03-Feb-2017 16:24:18 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 03-Feb-2017 16:24:18 Running on server: post build plugin 'Clover Delta Calculator' simple 03-Feb-2017 16:24:18 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 03-Feb-2017 16:24:18 All post build plugins have finished simple 03-Feb-2017 16:24:18 Generating build results summary... simple 03-Feb-2017 16:24:18 Saving build results to disk... simple 03-Feb-2017 16:24:18 Logging substituted variables... simple 03-Feb-2017 16:24:18 Indexing build results... simple 03-Feb-2017 16:24:18 Finished building CATS-MSC1-JOB1-2.