simple 29-Sep-2019 15:35:21 Build Clowder - pyclowder - bugfix-BD-2344-update-pip-in-simple-extractor-wrapper - Default Job #1 (CATS-PYC38-JOB1-1) started building on agent buildserver-2.os.ncsa.edu simple 29-Sep-2019 15:35:21 Remote agent on host buildserver-2.os.ncsa.edu simple 29-Sep-2019 15:35:21 Build working directory is /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC38-JOB1 simple 29-Sep-2019 15:35:21 Executing build Clowder - pyclowder - bugfix-BD-2344-update-pip-in-simple-extractor-wrapper - Default Job #1 (CATS-PYC38-JOB1-1) simple 29-Sep-2019 15:35:21 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 29-Sep-2019 15:35:21 Checking out into /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC38-JOB1 simple 29-Sep-2019 15:35:21 Updating source code to revision: 8c97747b1d0882a0524eb5885c4f82791a45c25d simple 29-Sep-2019 15:35:21 Creating local git repository in '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC38-JOB1/.git'. simple 29-Sep-2019 15:35:21 Initialized empty Git repository in /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC38-JOB1/.git/ simple 29-Sep-2019 15:35:22 Fetching 'refs/heads/bugfix/BD-2344-update-pip-in-simple-extractor-wrapper' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder.git'. Will try to do a shallow fetch. simple 29-Sep-2019 15:35:22 Warning: Permanently added '[127.0.0.1]:39245' (RSA) to the list of known hosts. simple 29-Sep-2019 15:35:22 From ssh://127.0.0.1:39245/cats/pyclowder simple 29-Sep-2019 15:35:22 * [new branch] bugfix/BD-2344-update-pip-in-simple-extractor-wrapper -> bugfix/BD-2344-update-pip-in-simple-extractor-wrapper simple 29-Sep-2019 15:35:22 Checking out revision 8c97747b1d0882a0524eb5885c4f82791a45c25d. simple 29-Sep-2019 15:35:22 Switched to branch 'bugfix/BD-2344-update-pip-in-simple-extractor-wrapper' simple 29-Sep-2019 15:35:22 Updated source code to revision: 8c97747b1d0882a0524eb5885c4f82791a45c25d simple 29-Sep-2019 15:35:22 Finished task 'Checkout Default Repository' with result: Success simple 29-Sep-2019 15:35:22 Running pre-build action: VCS Version Collector simple 29-Sep-2019 15:35:22 Starting task 'docker build and push' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 29-Sep-2019 15:35:22 Beginning to execute external process for build 'Clowder - pyclowder - bugfix-BD-2344-update-pip-in-simple-extractor-wrapper - Default Job #1 (CATS-PYC38-JOB1-1)'\n ... running command line: \n/bin/sh docker.sh\n ... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC38-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\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_capability_system_builder_command_buckminster_4_4=/home/bamboo/buckminster-4.4/buckminster\nbamboo_capability_system_builder_command_buckminster_4_2=/home/bamboo/buckminster-4.2/buckminster\nbamboo_planRepository_1_branchDisplayName=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\nbamboo_repository_revision_number=8c97747b1d0882a0524eb5885c4f82791a45c25d\nbamboo_resultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PYC38-JOB1-1\nbamboo_capability_system_builder_command_sphinx=/usr/bin/sphinx-build\nbamboo_build_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC38-JOB1\nbamboo_planRepository_1_name=pyclowder\nbamboo_buildKey=CATS-PYC38-JOB1\nbamboo_repository_177831954_name=pyclowder\nbamboo_capability_system_os=linux\nbamboo_shortPlanName=pyclowder\nbamboo_planRepository_name=pyclowder\nbamboo_repository_177831954_git_branch=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\nbamboo_buildNumber=1\nbamboo_capability_system_builder_node_grunt_6=/home/bamboo/node-v6.9.1/bin/grunt\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PYC38-JOB1-1\nbamboo_planRepository_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder.git\nbamboo_repository_177831954_git_username=\nbamboo_agentId=140673028\nbamboo_planName=Clowder - pyclowder - bugfix-BD-2344-update-pip-in-simple-extractor-wrapper\nbamboo_shortPlanKey=PYC38\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_repository_177831954_branch_name=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\nbamboo_planRepository_revision=8c97747b1d0882a0524eb5885c4f82791a45c25d\nbamboo_buildTimeStamp=2019-09-28T10:50:45.119-05:00\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_repository_git_branch=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\nbamboo_buildResultKey=CATS-PYC38-JOB1-1\nbamboo_repository_branch_name=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\nbamboo_buildPlanName=Clowder - pyclowder - bugfix-BD-2344-update-pip-in-simple-extractor-wrapper - Default Job\nbamboo_planRepository_1_revision=8c97747b1d0882a0524eb5885c4f82791a45c25d\nbamboo_capability_system_builder_command_python3=/usr/bin/python3\nbamboo_repository_name=pyclowder\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_repository_177831954_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder.git\nbamboo_planRepository_branch=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\nbamboo_agentWorkingDirectory=/home/bamboo/bamboo-agent-home/xml-data/build-dir\nbamboo_capability_system_git_executable=/usr/bin/git\nbamboo_repository_git_username=\nbamboo_capability_system_builder_sbt_SBT_0_13_13=/home/bamboo/sbt-0.13.13\nbamboo_planRepository_branchDisplayName=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\nbamboo_capability_system_builder_command_phantomjs=/home/bamboo/phantomjs-1.9.8/bin/phantomjs\nbamboo_planRepository_1_type=bbserver\nbamboo_planRepository_branchName=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\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-177700882\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/pyclowder.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-PYC38-JOB1\nbamboo_planKey=CATS-PYC38\nbamboo_repository_177831954_revision_number=8c97747b1d0882a0524eb5885c4f82791a45c25d\nbamboo_planRepository_1_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder.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=bugfix/BD-2344-update-pip-in-simple-extractor-wrapper\n build 29-Sep-2019 15:35:22 Sending build context to Docker daemon 264.2kB build 29-Sep-2019 15:35:22 build 29-Sep-2019 15:35:22 Step 1/9 : FROM ubuntu:16.04 build 29-Sep-2019 15:35:22 ---> 657d80a6401d build 29-Sep-2019 15:35:22 Step 2/9 : ENV RABBITMQ_URI="amqp://guest:guest@rabbitmq:5672/%2F" RABBITMQ_EXCHANGE="clowder" RABBITMQ_QUEUE="" REGISTRATION_ENDPOINTS="" EMAIL_SERVER="" EMAIL_SENDER="extractor" MAIN_SCRIPT="" build 29-Sep-2019 15:35:22 ---> Using cache build 29-Sep-2019 15:35:22 ---> d0185d2a2449 build 29-Sep-2019 15:35:22 Step 3/9 : RUN apt-get -q -q update && apt-get install -y --no-install-recommends python python-pip && pip install --upgrade setuptools && rm -rf /var/lib/apt/lists/* build 29-Sep-2019 15:35:22 ---> Using cache build 29-Sep-2019 15:35:22 ---> 46cac4521d03 build 29-Sep-2019 15:35:22 Step 4/9 : COPY pyclowder /tmp/pyclowder/pyclowder build 29-Sep-2019 15:35:22 ---> 43db4a8cd337 build 29-Sep-2019 15:35:22 Step 5/9 : COPY setup.py description.rst /tmp/pyclowder/ build 29-Sep-2019 15:35:23 ---> 459bfa9de516 build 29-Sep-2019 15:35:23 Step 6/9 : RUN pip install --upgrade /tmp/pyclowder && rm -rf /tmp/pyclowder build 29-Sep-2019 15:35:23 ---> Running in a91366307286 build 29-Sep-2019 15:35:24 Processing /tmp/pyclowder build 29-Sep-2019 15:35:25 Collecting enum34==1.1.6 (from pyclowder===2.1.1) build 29-Sep-2019 15:35:25 Downloading https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl build 29-Sep-2019 15:35:25 Collecting pika==1.0.0 (from pyclowder===2.1.1) build 29-Sep-2019 15:35:25 Downloading https://files.pythonhosted.org/packages/53/a4/5aff2293e1cdcf5f77447ebdfeaac99b622aef7d1e723cf9a5fe317b077c/pika-1.0.0-py2.py3-none-any.whl (148kB) build 29-Sep-2019 15:35:25 Collecting PyYAML==5.1 (from pyclowder===2.1.1) build 29-Sep-2019 15:35:25 Downloading https://files.pythonhosted.org/packages/9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d/PyYAML-5.1.tar.gz (274kB) build 29-Sep-2019 15:35:25 Collecting requests==2.21.0 (from pyclowder===2.1.1) build 29-Sep-2019 15:35:25 Downloading https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl (57kB) build 29-Sep-2019 15:35:25 Collecting certifi>=2017.4.17 (from requests==2.21.0->pyclowder===2.1.1) build 29-Sep-2019 15:35:25 Downloading https://files.pythonhosted.org/packages/18/b0/8146a4f8dd402f60744fa380bc73ca47303cccf8b9190fd16a827281eac2/certifi-2019.9.11-py2.py3-none-any.whl (154kB) build 29-Sep-2019 15:35:25 Collecting chardet<3.1.0,>=3.0.2 (from requests==2.21.0->pyclowder===2.1.1) build 29-Sep-2019 15:35:25 Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB) build 29-Sep-2019 15:35:25 Collecting idna<2.9,>=2.5 (from requests==2.21.0->pyclowder===2.1.1) build 29-Sep-2019 15:35:25 Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB) build 29-Sep-2019 15:35:26 Collecting urllib3<1.25,>=1.21.1 (from requests==2.21.0->pyclowder===2.1.1) build 29-Sep-2019 15:35:26 Downloading https://files.pythonhosted.org/packages/01/11/525b02e4acc0c747de8b6ccdab376331597c569c42ea66ab0a1dbd36eca2/urllib3-1.24.3-py2.py3-none-any.whl (118kB) build 29-Sep-2019 15:35:26 Building wheels for collected packages: PyYAML build 29-Sep-2019 15:35:26 Running setup.py bdist_wheel for PyYAML: started build 29-Sep-2019 15:35:26 Running setup.py bdist_wheel for PyYAML: finished with status 'error' build 29-Sep-2019 15:35:26 Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-6yLx09/PyYAML/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /tmp/tmpFeZE7Dpip-wheel- --python-tag cp27: build 29-Sep-2019 15:35:26 usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] build 29-Sep-2019 15:35:26 or: -c --help [cmd1 cmd2 ...] build 29-Sep-2019 15:35:26 or: -c --help-commands build 29-Sep-2019 15:35:26 or: -c cmd --help build 29-Sep-2019 15:35:26 build 29-Sep-2019 15:35:26 error: invalid command 'bdist_wheel' build 29-Sep-2019 15:35:26 build 29-Sep-2019 15:35:26 ---------------------------------------- build 29-Sep-2019 15:35:26  Failed building wheel for PyYAML build 29-Sep-2019 15:35:26  Running setup.py clean for PyYAML build 29-Sep-2019 15:35:26 Failed to build PyYAML build 29-Sep-2019 15:35:26 Installing collected packages: enum34, pika, PyYAML, certifi, chardet, idna, urllib3, requests, pyclowder build 29-Sep-2019 15:35:26 Running setup.py install for PyYAML: started build 29-Sep-2019 15:35:26 Running setup.py install for PyYAML: finished with status 'done' build 29-Sep-2019 15:35:27 Running setup.py install for pyclowder: started build 29-Sep-2019 15:35:27 Running setup.py install for pyclowder: finished with status 'done' build 29-Sep-2019 15:35:27 Successfully installed PyYAML-5.1 certifi-2019.9.11 chardet-3.0.4 enum34-1.1.6 idna-2.8 pika-1.0.0 pyclowder-2.1.1 requests-2.21.0 urllib3-1.24.3 build 29-Sep-2019 15:35:27 You are using pip version 8.1.1, however version 19.2.3 is available. build 29-Sep-2019 15:35:27 You should consider upgrading via the 'pip install --upgrade pip' command. build 29-Sep-2019 15:35:28 Removing intermediate container a91366307286 build 29-Sep-2019 15:35:28 ---> 0c5462291f53 build 29-Sep-2019 15:35:28 Step 7/9 : WORKDIR /home/clowder build 29-Sep-2019 15:35:28 ---> Running in 61694979c948 build 29-Sep-2019 15:35:29 Removing intermediate container 61694979c948 build 29-Sep-2019 15:35:29 ---> 3d5e1b4f539e build 29-Sep-2019 15:35:29 Step 8/9 : COPY notifications.json /home/clowder build 29-Sep-2019 15:35:29 ---> dbb136a93bdb build 29-Sep-2019 15:35:29 Step 9/9 : CMD python "./${MAIN_SCRIPT}" build 29-Sep-2019 15:35:30 ---> Running in 392120884fdf build 29-Sep-2019 15:35:30 Removing intermediate container 392120884fdf build 29-Sep-2019 15:35:30 ---> 7d95282dea62 build 29-Sep-2019 15:35:30 Successfully built 7d95282dea62 build 29-Sep-2019 15:35:30 Successfully tagged clowder/pyclowder:latest build 29-Sep-2019 15:35:30 Sending build context to Docker daemon 262.7kB build 29-Sep-2019 15:35:30 build 29-Sep-2019 15:35:30 Step 1/6 : FROM clowder/pyclowder build 29-Sep-2019 15:35:30 ---> 7d95282dea62 build 29-Sep-2019 15:35:30 Step 2/6 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 15:35:30 ---> Running in 041c36992ab0 build 29-Sep-2019 15:35:31 Removing intermediate container 041c36992ab0 build 29-Sep-2019 15:35:31 ---> f2595e11b6a8 build 29-Sep-2019 15:35:31 Step 3/6 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 15:35:31 ---> Running in e06c1434110b build 29-Sep-2019 15:35:31 Removing intermediate container e06c1434110b build 29-Sep-2019 15:35:31 ---> 0cb68c689e09 build 29-Sep-2019 15:35:31 Step 4/6 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 29-Sep-2019 15:35:31 ---> Running in daeca987a3f5 build 29-Sep-2019 15:35:32 Removing intermediate container daeca987a3f5 build 29-Sep-2019 15:35:32 ---> 59cf5945c932 build 29-Sep-2019 15:35:32 Step 5/6 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 29-Sep-2019 15:35:32 ---> Running in 8ca2393c33d8 build 29-Sep-2019 15:35:32 Removing intermediate container 8ca2393c33d8 build 29-Sep-2019 15:35:32 ---> 325de8061521 build 29-Sep-2019 15:35:32 Step 6/6 : ONBUILD ADD . /home/clowder/ build 29-Sep-2019 15:35:33 ---> Running in b814cfcf0fb7 build 29-Sep-2019 15:35:33 Removing intermediate container b814cfcf0fb7 build 29-Sep-2019 15:35:33 ---> b9c3abcac832 build 29-Sep-2019 15:35:33 Successfully built b9c3abcac832 build 29-Sep-2019 15:35:33 Successfully tagged clowder/pyclowder:onbuild build 29-Sep-2019 15:35:33 Sending build context to Docker daemon 12.8kB build 29-Sep-2019 15:35:33 build 29-Sep-2019 15:35:33 Step 1/5 : FROM clowder/pyclowder:onbuild build 29-Sep-2019 15:35:33 # Executing 5 build triggers build 29-Sep-2019 15:35:34 ---> Running in a13df48bcb14 build 29-Sep-2019 15:35:36 Removing intermediate container a13df48bcb14 build 29-Sep-2019 15:35:36 ---> Running in edab5fd26f3f build 29-Sep-2019 15:35:39 Removing intermediate container edab5fd26f3f build 29-Sep-2019 15:35:39 ---> 8ab4d38f4feb build 29-Sep-2019 15:35:39 Step 2/5 : ENV MAIN_SCRIPT="binary_extractor.py" RABBITMQ_QUEUE="" IMAGE_BINARY="" IMAGE_TYPE="" IMAGE_THUMBNAIL_COMMAND="" IMAGE_PREVIEW_COMMAND="" PREVIEW_BINARY="" PREVIEW_TYPE="" PREVIEW_COMMAND="" build 29-Sep-2019 15:35:40 ---> Running in f56971872ef0 build 29-Sep-2019 15:35:40 Removing intermediate container f56971872ef0 build 29-Sep-2019 15:35:40 ---> 540d0ea7b187 build 29-Sep-2019 15:35:40 Step 3/5 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 15:35:40 ---> Running in e95f2c2bdba7 build 29-Sep-2019 15:35:40 Removing intermediate container e95f2c2bdba7 build 29-Sep-2019 15:35:40 ---> f2f23a3bd74f build 29-Sep-2019 15:35:40 Step 4/5 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 15:35:40 ---> Running in c6a3b6ea6091 build 29-Sep-2019 15:35:41 Removing intermediate container c6a3b6ea6091 build 29-Sep-2019 15:35:41 ---> acab6ac98073 build 29-Sep-2019 15:35:41 Step 5/5 : ONBUILD COPY extractor_info.json /home/clowder/ build 29-Sep-2019 15:35:41 ---> Running in a995b1a4012c build 29-Sep-2019 15:35:41 Removing intermediate container a995b1a4012c build 29-Sep-2019 15:35:41 ---> 671d412b75ac build 29-Sep-2019 15:35:41 Successfully built 671d412b75ac build 29-Sep-2019 15:35:41 Successfully tagged clowder/extractors-binary-preview:onbuild build 29-Sep-2019 15:35:41 Sending build context to Docker daemon 6.656kB build 29-Sep-2019 15:35:41 build 29-Sep-2019 15:35:41 Step 1/9 : FROM clowder/pyclowder:onbuild build 29-Sep-2019 15:35:41 # Executing 5 build triggers build 29-Sep-2019 15:35:42 ---> Running in b9aecb9d2891 build 29-Sep-2019 15:35:47 Removing intermediate container b9aecb9d2891 build 29-Sep-2019 15:35:48 ---> Running in 8a85e5763719 build 29-Sep-2019 15:35:49 Removing intermediate container 8a85e5763719 build 29-Sep-2019 15:35:50 ---> f92adb0c865d build 29-Sep-2019 15:35:50 Step 2/9 : ENV EXTRACTION_FUNC="" build 29-Sep-2019 15:35:50 ---> Running in 8638aaf8ec3c build 29-Sep-2019 15:35:50 Removing intermediate container 8638aaf8ec3c build 29-Sep-2019 15:35:50 ---> 917bdf425ad4 build 29-Sep-2019 15:35:50 Step 3/9 : ENV EXTRACTION_MODULE="" build 29-Sep-2019 15:35:50 ---> Running in bdb1f951abc4 build 29-Sep-2019 15:35:51 Removing intermediate container bdb1f951abc4 build 29-Sep-2019 15:35:51 ---> 5ca5e34da548 build 29-Sep-2019 15:35:51 Step 4/9 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 29-Sep-2019 15:35:52 ---> Running in 3a33e8f85a3f build 29-Sep-2019 15:35:52 Removing intermediate container 3a33e8f85a3f build 29-Sep-2019 15:35:52 ---> 5c8d8a334688 build 29-Sep-2019 15:35:52 Step 5/9 : ONBUILD RUN if [ -e packages.apt ]; then apt-get -q -q update && xargs apt-get -y install --no-install-recommends < packages.apt && rm -rf /var/lib/apt/lists/*; fi build 29-Sep-2019 15:35:52 ---> Running in d22298d1e5aa build 29-Sep-2019 15:35:53 Removing intermediate container d22298d1e5aa build 29-Sep-2019 15:35:53 ---> 42c1c2ca6851 build 29-Sep-2019 15:35:53 Step 6/9 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 29-Sep-2019 15:35:53 ---> Running in 877a80fb2538 build 29-Sep-2019 15:35:53 Removing intermediate container 877a80fb2538 build 29-Sep-2019 15:35:53 ---> df8648b33bd6 build 29-Sep-2019 15:35:53 Step 7/9 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 29-Sep-2019 15:35:53 ---> Running in c1c101453e53 build 29-Sep-2019 15:35:54 Removing intermediate container c1c101453e53 build 29-Sep-2019 15:35:54 ---> 7bc20008faad build 29-Sep-2019 15:35:54 Step 8/9 : ONBUILD ADD . /home/clowder/ build 29-Sep-2019 15:35:54 ---> Running in b72caa234380 build 29-Sep-2019 15:35:55 Removing intermediate container b72caa234380 build 29-Sep-2019 15:35:55 ---> 85a3a9220ffd build 29-Sep-2019 15:35:55 Step 9/9 : CMD python -c "from simple_extractor import SimplePythonExtractor; from ${EXTRACTION_MODULE} import *; SimplePythonExtractor(${EXTRACTION_FUNC}).start()" build 29-Sep-2019 15:35:55 ---> Running in b82f871f646f build 29-Sep-2019 15:35:55 Removing intermediate container b82f871f646f build 29-Sep-2019 15:35:55 ---> 0c2b39f9ee56 build 29-Sep-2019 15:35:55 Successfully built 0c2b39f9ee56 build 29-Sep-2019 15:35:55 Successfully tagged clowder/extractors-simple-extractor:onbuild build 29-Sep-2019 15:35:55 Sending build context to Docker daemon 13.31kB build 29-Sep-2019 15:35:55 build 29-Sep-2019 15:35:55 Step 1/10 : FROM clowder/pyclowder:latest build 29-Sep-2019 15:35:55 ---> 7d95282dea62 build 29-Sep-2019 15:35:55 Step 2/10 : ENV R_SCRIPT="" R_FUNCTION="" build 29-Sep-2019 15:35:56 ---> Running in 91c339be4df7 build 29-Sep-2019 15:35:56 Removing intermediate container 91c339be4df7 build 29-Sep-2019 15:35:56 ---> bb211937ff43 build 29-Sep-2019 15:35:56 Step 3/10 : RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" > /etc/apt/sources.list.d/R.list && apt-key adv --keyserver keyserver.ubuntu.com --recv E084DAB9 && apt-get -q -q update && apt-get -y install --no-install-recommends r-base-core r-base-dev && rm -rf /var/lib/apt/lists/* && Rscript --vanilla -e "install.packages('jsonlite', repos='http://cran.rstudio.com/'); print(system.file(package = 'jsonlite')); q(status=as.integer(system.file(package = 'jsonlite') == ''))" build 29-Sep-2019 15:35:56 ---> Running in 09a203d4924a build 29-Sep-2019 15:35:57 Executing: /tmp/tmp.zHlctM3Bsb/gpg.1.sh --keyserver build 29-Sep-2019 15:35:57 keyserver.ubuntu.com build 29-Sep-2019 15:35:57 --recv build 29-Sep-2019 15:35:57 E084DAB9 build 29-Sep-2019 15:35:57 gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com build 29-Sep-2019 15:35:57 gpg: key E084DAB9: public key "Totally Legit Signing Key " imported build 29-Sep-2019 15:35:57 gpg: Total number processed: 1 build 29-Sep-2019 15:35:57 gpg: imported: 1 (RSA: 1) build 29-Sep-2019 15:36:05 W: GPG error: http://cran.rstudio.com/bin/linux/ubuntu xenial/ InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 51716619E084DAB9 build 29-Sep-2019 15:36:05 W: The repository 'http://cran.rstudio.com/bin/linux/ubuntu xenial/ InRelease' is not signed. build 29-Sep-2019 15:36:06 Reading package lists... build 29-Sep-2019 15:36:06 Building dependency tree... build 29-Sep-2019 15:36:06 Reading state information... build 29-Sep-2019 15:36:07 The following additional packages will be installed: build 29-Sep-2019 15:36:07 autoconf automake autotools-dev binutils bsdmainutils build-essential bzip2 build 29-Sep-2019 15:36:07 cdbs cpp cpp-5 debhelper dh-strip-nondeterminism dh-translations dpkg-dev build 29-Sep-2019 15:36:07 file fontconfig fontconfig-config fonts-dejavu-core g++ g++-5 gcc gcc-5 build 29-Sep-2019 15:36:07 gettext gettext-base gfortran gfortran-5 groff-base icu-devtools intltool build 29-Sep-2019 15:36:07 intltool-debian libarchive-zip-perl libasan2 libasn1-8-heimdal build 29-Sep-2019 15:36:07 libasprintf0v5 libatomic1 libblas-common libblas-dev libblas3 libbz2-dev build 29-Sep-2019 15:36:07 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcilkrts5 libcroco3 libcurl3 build 29-Sep-2019 15:36:07 libdatrie1 libdpkg-perl libencode-locale-perl libfile-listing-perl build 29-Sep-2019 15:36:07 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-5-dev build 29-Sep-2019 15:36:07 libgdbm3 libgfortran-5-dev libgfortran3 libglib2.0-0 libgmp10 libgnutls30 build 29-Sep-2019 15:36:07 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b build 29-Sep-2019 15:36:07 libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 build 29-Sep-2019 15:36:07 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl build 29-Sep-2019 15:36:07 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl build 29-Sep-2019 15:36:07 libhttp-negotiate-perl libhx509-5-heimdal libice6 libicu-dev libicu55 build 29-Sep-2019 15:36:07 libidn11 libio-html-perl libio-socket-ssl-perl libisl15 libitm1 libjbig0 build 29-Sep-2019 15:36:07 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev build 29-Sep-2019 15:36:07 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 build 29-Sep-2019 15:36:07 liblapack-dev liblapack3 libldap-2.4-2 liblsan0 liblwp-mediatypes-perl build 29-Sep-2019 15:36:07 liblwp-protocol-https-perl liblzma-dev libmagic1 libmpc3 libmpfr4 libmpx0 build 29-Sep-2019 15:36:07 libncurses5-dev libnet-http-perl libnet-ssleay-perl libnettle6 libp11-kit0 build 29-Sep-2019 15:36:07 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils build 29-Sep-2019 15:36:07 libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libperl5.22 build 29-Sep-2019 15:36:07 libpipeline1 libpixman-1-0 libpng12-0 libpng12-dev libquadmath0 build 29-Sep-2019 15:36:07 libreadline-dev libreadline6-dev libroken18-heimdal librtmp1 libsasl2-2 build 29-Sep-2019 15:36:07 libsasl2-modules-db libsigsegv2 libsm6 libstdc++-5-dev libtasn1-6 libtcl8.6 build 29-Sep-2019 15:36:07 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 build 29-Sep-2019 15:36:07 libtsan0 libubsan0 libunistring0 liburi-perl libwind0-heimdal libwww-perl build 29-Sep-2019 15:36:07 libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 build 29-Sep-2019 15:36:07 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml2 build 29-Sep-2019 15:36:07 libxmuu1 libxrender1 libxss1 libxt6 linux-libc-dev m4 make man-db netbase build 29-Sep-2019 15:36:07 patch perl perl-modules-5.22 pkg-config po-debconf python-pkg-resources build 29-Sep-2019 15:36:07 python-scour python-six tzdata ucf unzip x11-common xauth xdg-utils xz-utils build 29-Sep-2019 15:36:07 zip zlib1g-dev build 29-Sep-2019 15:36:07 Suggested packages: build 29-Sep-2019 15:36:07 autoconf-archive gnu-standards autoconf-doc libtool binutils-doc wamerican build 29-Sep-2019 15:36:07 | wordlist whois vacation bzip2-doc devscripts cpp-doc gcc-5-locales dh-make build 29-Sep-2019 15:36:07 debian-keyring g++-multilib g++-5-multilib gcc-5-doc libstdc++6-5-dbg build 29-Sep-2019 15:36:07 gcc-multilib manpages-dev flex bison gdb gcc-doc gcc-5-multilib libgcc1-dbg build 29-Sep-2019 15:36:07 libgomp1-dbg libitm1-dbg libatomic1-dbg libasan2-dbg liblsan0-dbg build 29-Sep-2019 15:36:07 libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx0-dbg libquadmath0-dbg build 29-Sep-2019 15:36:07 gettext-doc autopoint gfortran-multilib gfortran-doc gfortran-5-multilib build 29-Sep-2019 15:36:07 gfortran-5-doc libgfortran3-dbg groff liblapack-doc-man liblapack-doc build 29-Sep-2019 15:36:07 glibc-doc gnutls-bin krb5-doc krb5-user libdata-dump-perl icu-doc build 29-Sep-2019 15:36:07 libcrypt-ssleay-perl liblzma-doc ncurses-doc readline-doc libstdc++-5-doc build 29-Sep-2019 15:36:07 tcl8.6 tk8.6 libauthen-ntlm-perl make-doc less www-browser ed diffutils-doc build 29-Sep-2019 15:36:07 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl build 29-Sep-2019 15:36:07 libmail-box-perl python-setuptools python-rsvg python-cairo ess r-doc-info build 29-Sep-2019 15:36:07 | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base build 29-Sep-2019 15:36:07 texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra build 29-Sep-2019 15:36:07 texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo build 29-Sep-2019 15:36:07 gvfs-bin build 29-Sep-2019 15:36:07 Recommended packages: build 29-Sep-2019 15:36:07 fakeroot libalgorithm-merge-perl curl | wget | lynx-cur libasprintf-dev build 29-Sep-2019 15:36:07 libgettextpo-dev bzip2-doc manpages manpages-dev libfile-fcntllock-perl build 29-Sep-2019 15:36:07 libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl build 29-Sep-2019 15:36:07 krb5-locales libsasl2-modules libhtml-form-perl libhttp-daemon-perl build 29-Sep-2019 15:36:07 libmailtools-perl xml-core ifupdown rename libmail-sendmail-perl build 29-Sep-2019 15:36:07 r-recommended r-doc-html libfile-mimeinfo-perl libnet-dbus-perl build 29-Sep-2019 15:36:07 libx11-protocol-perl x11-utils x11-xserver-utils build 29-Sep-2019 15:36:07 The following NEW packages will be installed: build 29-Sep-2019 15:36:07 autoconf automake autotools-dev binutils bsdmainutils build-essential bzip2 build 29-Sep-2019 15:36:07 cdbs cpp cpp-5 debhelper dh-strip-nondeterminism dh-translations dpkg-dev build 29-Sep-2019 15:36:07 file fontconfig fontconfig-config fonts-dejavu-core g++ g++-5 gcc gcc-5 build 29-Sep-2019 15:36:07 gettext gettext-base gfortran gfortran-5 groff-base icu-devtools intltool build 29-Sep-2019 15:36:07 intltool-debian libarchive-zip-perl libasan2 libasn1-8-heimdal build 29-Sep-2019 15:36:07 libasprintf0v5 libatomic1 libblas-common libblas-dev libblas3 libbz2-dev build 29-Sep-2019 15:36:07 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcilkrts5 libcroco3 libcurl3 build 29-Sep-2019 15:36:07 libdatrie1 libdpkg-perl libencode-locale-perl libfile-listing-perl build 29-Sep-2019 15:36:07 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-5-dev build 29-Sep-2019 15:36:07 libgdbm3 libgfortran-5-dev libgfortran3 libglib2.0-0 libgmp10 libgnutls30 build 29-Sep-2019 15:36:07 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b build 29-Sep-2019 15:36:07 libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 build 29-Sep-2019 15:36:07 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl build 29-Sep-2019 15:36:07 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl build 29-Sep-2019 15:36:07 libhttp-negotiate-perl libhx509-5-heimdal libice6 libicu-dev libicu55 build 29-Sep-2019 15:36:07 libidn11 libio-html-perl libio-socket-ssl-perl libisl15 libitm1 libjbig0 build 29-Sep-2019 15:36:07 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev build 29-Sep-2019 15:36:07 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 build 29-Sep-2019 15:36:07 liblapack-dev liblapack3 libldap-2.4-2 liblsan0 liblwp-mediatypes-perl build 29-Sep-2019 15:36:07 liblwp-protocol-https-perl liblzma-dev libmagic1 libmpc3 libmpfr4 libmpx0 build 29-Sep-2019 15:36:07 libncurses5-dev libnet-http-perl libnet-ssleay-perl libnettle6 libp11-kit0 build 29-Sep-2019 15:36:07 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils build 29-Sep-2019 15:36:07 libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libperl5.22 build 29-Sep-2019 15:36:07 libpipeline1 libpixman-1-0 libpng12-0 libpng12-dev libquadmath0 build 29-Sep-2019 15:36:07 libreadline-dev libreadline6-dev libroken18-heimdal librtmp1 libsasl2-2 build 29-Sep-2019 15:36:07 libsasl2-modules-db libsigsegv2 libsm6 libstdc++-5-dev libtasn1-6 libtcl8.6 build 29-Sep-2019 15:36:07 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 build 29-Sep-2019 15:36:07 libtsan0 libubsan0 libunistring0 liburi-perl libwind0-heimdal libwww-perl build 29-Sep-2019 15:36:07 libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 build 29-Sep-2019 15:36:07 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml2 build 29-Sep-2019 15:36:07 libxmuu1 libxrender1 libxss1 libxt6 linux-libc-dev m4 make man-db netbase build 29-Sep-2019 15:36:07 patch perl perl-modules-5.22 pkg-config po-debconf python-pkg-resources build 29-Sep-2019 15:36:07 python-scour python-six r-base-core r-base-dev tzdata ucf unzip x11-common build 29-Sep-2019 15:36:07 xauth xdg-utils xz-utils zip zlib1g-dev build 29-Sep-2019 15:36:07 0 upgraded, 190 newly installed, 0 to remove and 0 not upgraded. build 29-Sep-2019 15:36:07 Need to get 116 MB of archives. build 29-Sep-2019 15:36:07 After this operation, 416 MB of additional disk space will be used. build 29-Sep-2019 15:36:07 WARNING: The following packages cannot be authenticated! build 29-Sep-2019 15:36:07 r-base-core r-base-dev build 29-Sep-2019 15:36:07 E: There were unauthenticated packages and -y was used without --allow-unauthenticated error 29-Sep-2019 15:36:07 The command '/bin/sh -c echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" > /etc/apt/sources.list.d/R.list && apt-key adv --keyserver keyserver.ubuntu.com --recv E084DAB9 && apt-get -q -q update && apt-get -y install --no-install-recommends r-base-core r-base-dev && rm -rf /var/lib/apt/lists/* && Rscript --vanilla -e "install.packages('jsonlite', repos='http://cran.rstudio.com/'); print(system.file(package = 'jsonlite')); q(status=as.integer(system.file(package = 'jsonlite') == ''))"' returned a non-zero code: 100 build 29-Sep-2019 15:36:07  simple 29-Sep-2019 15:36:07 Failing task since return code of [/bin/sh docker.sh] was 100 while expected 0 simple 29-Sep-2019 15:36:07 Finished task 'docker build and push' with result: Failed simple 29-Sep-2019 15:36:07 Running post build plugin 'Docker Container Cleanup' simple 29-Sep-2019 15:36:07 Running post build plugin 'NCover Results Collector' simple 29-Sep-2019 15:36:07 Running post build plugin 'Clover Results Collector' simple 29-Sep-2019 15:36:07 Running post build plugin 'npm Cache Cleanup' simple 29-Sep-2019 15:36:07 Running post build plugin 'Artifact Copier' simple 29-Sep-2019 15:36:07 Finalising the build... simple 29-Sep-2019 15:36:07 Stopping timer. simple 29-Sep-2019 15:36:07 Build CATS-PYC38-JOB1-1 completed. simple 29-Sep-2019 15:36:07 Running on server: post build plugin 'NCover Results Collector' simple 29-Sep-2019 15:36:07 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 29-Sep-2019 15:36:07 Running on server: post build plugin 'Clover Delta Calculator' simple 29-Sep-2019 15:36:07 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 29-Sep-2019 15:36:07 All post build plugins have finished simple 29-Sep-2019 15:36:07 Generating build results summary... simple 29-Sep-2019 15:36:08 Saving build results to disk... simple 29-Sep-2019 15:36:08 Logging substituted variables... simple 29-Sep-2019 15:36:08 Indexing build results... simple 29-Sep-2019 15:36:08 Finished building CATS-PYC38-JOB1-1.