simple 30-May-2019 23:21:47 Build Clowder - pyclowder2 - bugfix-BD-2345-open-extractor-info-json-with-utf-8-encoding - Default Job #2 (CATS-PYC299-JOB1-2) started building on agent buildserver-3.os.ncsa.edu simple 30-May-2019 23:21:47 Remote agent on host buildserver-3.os.ncsa.edu simple 30-May-2019 23:21:47 Build working directory is /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1 simple 30-May-2019 23:21:47 Executing build Clowder - pyclowder2 - bugfix-BD-2345-open-extractor-info-json-with-utf-8-encoding - Default Job #2 (CATS-PYC299-JOB1-2) simple 30-May-2019 23:21:47 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 30-May-2019 23:21:47 Checking out into /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1 simple 30-May-2019 23:21:47 Updating source code to revision: a54e1410f4217209bc72e2af5b2266ead7d08a0d simple 30-May-2019 23:21:47 Creating local git repository in '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1/.git'. simple 30-May-2019 23:21:47 Initialized empty Git repository in /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1/.git/ simple 30-May-2019 23:21:47 Fetching 'refs/heads/bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder2.git'. Will try to do a shallow fetch. simple 30-May-2019 23:21:47 Warning: Permanently added '[127.0.0.1]:42919' (RSA) to the list of known hosts. simple 30-May-2019 23:21:48 From ssh://127.0.0.1:42919/cats/pyclowder2 simple 30-May-2019 23:21:48 * [new branch] bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding -> bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding simple 30-May-2019 23:21:48 Checking out revision a54e1410f4217209bc72e2af5b2266ead7d08a0d. simple 30-May-2019 23:21:48 Switched to branch 'bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding' simple 30-May-2019 23:21:48 Updated source code to revision: a54e1410f4217209bc72e2af5b2266ead7d08a0d simple 30-May-2019 23:21:48 Finished task 'Checkout Default Repository' with result: Success simple 30-May-2019 23:21:48 Running pre-build action: VCS Version Collector simple 30-May-2019 23:21:48 Starting task 'python 2 - pytest' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 30-May-2019 23:21:48 Beginning to execute external process for build 'Clowder - 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Installing collected packages: enum34, pika, PyYAML, certifi, chardet, idna, urllib3, requests, wheel, atomicwrites, py, six, scandir, pathlib2, configparser, contextlib2, zipp, importlib-metadata, pluggy, attrs, more-itertools, funcsigs, pytest, pep8, apipkg, execnet, pytest-cache, pytest-pep8 build 30-May-2019 23:21:53 Found existing installation: wheel 0.33.4 build 30-May-2019 23:21:53 Uninstalling wheel-0.33.4: build 30-May-2019 23:21:53 Successfully uninstalled wheel-0.33.4 build 30-May-2019 23:21:53 Successfully installed PyYAML-5.1 apipkg-1.5 atomicwrites-1.3.0 attrs-19.1.0 certifi-2019.3.9 chardet-3.0.4 configparser-3.7.4 contextlib2-0.5.5 enum34-1.1.6 execnet-1.6.0 funcsigs-1.0.2 idna-2.8 importlib-metadata-0.17 more-itertools-5.0.0 pathlib2-2.3.3 pep8-1.7.1 pika-1.0.0 pluggy-0.12.0 py-1.8.0 pytest-4.3.1 pytest-cache-1.0 pytest-pep8-1.0.6 requests-2.21.0 scandir-1.10.0 six-1.12.0 urllib3-1.24.1 wheel-0.33.1 zipp-0.5.1 build 30-May-2019 23:21:54 ============================= test session starts ============================== build 30-May-2019 23:21:54 platform linux2 -- Python 2.7.12, pytest-4.3.1, py-1.8.0, pluggy-0.12.0 build 30-May-2019 23:21:54 rootdir: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1, inifile: setup.cfg build 30-May-2019 23:21:54 plugins: pep8-1.0.6 build 30-May-2019 23:21:54 collected 20 items build 30-May-2019 23:21:54 build 30-May-2019 23:21:54 setup.py . build 30-May-2019 23:21:54 contrib/monitor/monitor.py . build 30-May-2019 23:21:54 docs/source/conf.py . build 30-May-2019 23:21:54 pyclowder/__init__.py . build 30-May-2019 23:21:54 pyclowder/client.py . build 30-May-2019 23:21:54 pyclowder/collections.py . build 30-May-2019 23:21:54 pyclowder/connectors.py . build 30-May-2019 23:21:54 pyclowder/datasets.py . build 30-May-2019 23:21:54 pyclowder/extractors.py . build 30-May-2019 23:21:54 pyclowder/files.py . build 30-May-2019 23:21:54 pyclowder/geostreams.py . build 30-May-2019 23:21:54 pyclowder/sections.py . build 30-May-2019 23:21:54 pyclowder/utils.py . build 30-May-2019 23:21:54 sample-extractors/binary-preview/binary_extractor.py . build 30-May-2019 23:21:54 sample-extractors/echo/echo.py . build 30-May-2019 23:21:54 sample-extractors/simple-extractor/simple_extractor.py . build 30-May-2019 23:21:54 sample-extractors/simple-r-extractor/r_extractor.py . build 30-May-2019 23:21:54 sample-extractors/wordcount/wordcount.py . build 30-May-2019 23:21:54 sample-extractors/wordcount-simple-extractor/wordcount.py . build 30-May-2019 23:21:54 tests/clientTest.py . build 30-May-2019 23:21:54 build 30-May-2019 23:21:54 - generated xml file: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1/test-reports/results-p2.xml - build 30-May-2019 23:21:54 ========================== 20 passed in 0.44 seconds =========================== simple 30-May-2019 23:21:54 Finished task 'python 2 - pytest' with result: Success simple 30-May-2019 23:21:54 Starting task 'python 3 - pytest' of type 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build 30-May-2019 23:21:54 Already using interpreter /usr/bin/python3 build 30-May-2019 23:21:54 Using base prefix '/usr' build 30-May-2019 23:21:54 New python executable in /tmp/virtualenv/pyclowder2-p3/bin/python3 build 30-May-2019 23:21:54 Also creating executable in /tmp/virtualenv/pyclowder2-p3/bin/python build 30-May-2019 23:21:57 Installing setuptools, pkg_resources, pip, wheel...done. build 30-May-2019 23:21:58 Collecting enum34==1.1.6 (from -r requirements.txt (line 1)) build 30-May-2019 23:21:58 Using cached https://files.pythonhosted.org/packages/af/42/cb9355df32c69b553e72a2e28daee25d1611d2c0d9c272aa1d34204205b2/enum34-1.1.6-py3-none-any.whl build 30-May-2019 23:21:58 Collecting pika==1.0.0 (from -r requirements.txt (line 2)) build 30-May-2019 23:21:58 Using cached https://files.pythonhosted.org/packages/53/a4/5aff2293e1cdcf5f77447ebdfeaac99b622aef7d1e723cf9a5fe317b077c/pika-1.0.0-py2.py3-none-any.whl build 30-May-2019 23:21:58 Collecting PyYAML==5.1 (from -r 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build 30-May-2019 23:21:59 Using cached https://files.pythonhosted.org/packages/7f/72/5e13a37e989bdb54ac3f52808e122cbd9b878ac980f932dc237ff64f8a00/importlib_metadata-0.17-py2.py3-none-any.whl build 30-May-2019 23:21:59 Collecting execnet>=1.1.dev1 (from pytest-cache->pytest-pep8==1.0.6->-r requirements.txt (line 8)) build 30-May-2019 23:21:59 Using cached https://files.pythonhosted.org/packages/77/1a/f69e1f73bc36f55d3273afd1c52936def71ac67d9c5215be3a4ca3a45577/execnet-1.6.0-py2.py3-none-any.whl build 30-May-2019 23:21:59 Collecting zipp>=0.5 (from importlib-metadata>=0.12->pluggy>=0.7->pytest==4.3.1->-r requirements.txt (line 7)) build 30-May-2019 23:21:59 Using cached https://files.pythonhosted.org/packages/a0/0f/9bf71d438d2e9d5fd0e4569ea4d1a2b6f5a524c234c6d221b494298bb4d1/zipp-0.5.1-py2.py3-none-any.whl build 30-May-2019 23:21:59 Collecting apipkg>=1.4 (from execnet>=1.1.dev1->pytest-cache->pytest-pep8==1.0.6->-r requirements.txt (line 8)) build 30-May-2019 23:21:59 Using cached 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30-May-2019 23:22:00 ============================= test session starts ============================== build 30-May-2019 23:22:00 platform linux -- Python 3.5.2, pytest-4.3.1, py-1.8.0, pluggy-0.12.0 build 30-May-2019 23:22:00 rootdir: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1, inifile: setup.cfg build 30-May-2019 23:22:00 plugins: pep8-1.0.6 build 30-May-2019 23:22:00 collected 20 items build 30-May-2019 23:22:00 build 30-May-2019 23:22:00 setup.py . build 30-May-2019 23:22:00 contrib/monitor/monitor.py . build 30-May-2019 23:22:00 docs/source/conf.py . build 30-May-2019 23:22:00 pyclowder/__init__.py . build 30-May-2019 23:22:00 pyclowder/client.py . build 30-May-2019 23:22:01 pyclowder/collections.py . build 30-May-2019 23:22:01 pyclowder/connectors.py . build 30-May-2019 23:22:01 pyclowder/datasets.py . build 30-May-2019 23:22:01 pyclowder/extractors.py . build 30-May-2019 23:22:01 pyclowder/files.py . build 30-May-2019 23:22:01 pyclowder/geostreams.py . build 30-May-2019 23:22:01 pyclowder/sections.py . build 30-May-2019 23:22:01 pyclowder/utils.py . build 30-May-2019 23:22:01 sample-extractors/binary-preview/binary_extractor.py . build 30-May-2019 23:22:01 sample-extractors/echo/echo.py . build 30-May-2019 23:22:01 sample-extractors/simple-extractor/simple_extractor.py . build 30-May-2019 23:22:01 sample-extractors/simple-r-extractor/r_extractor.py . build 30-May-2019 23:22:01 sample-extractors/wordcount/wordcount.py . build 30-May-2019 23:22:01 sample-extractors/wordcount-simple-extractor/wordcount.py . build 30-May-2019 23:22:01 tests/clientTest.py . build 30-May-2019 23:22:01 build 30-May-2019 23:22:01 - generated xml file: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1/test-reports/results-p3.xml - build 30-May-2019 23:22:01 ========================== 20 passed in 0.53 seconds =========================== simple 30-May-2019 23:22:01 Finished task 'python 3 - pytest' with result: Success simple 30-May-2019 23:22:01 Starting task 'docker build' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 30-May-2019 23:22:01 Beginning to execute external process for build 'Clowder - pyclowder2 - bugfix-BD-2345-open-extractor-info-json-with-utf-8-encoding - Default Job #2 (CATS-PYC299-JOB1-2)'\n ... running command line: \n/bin/sh docker.sh\n ... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1\n ... using extra environment variables: 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build 30-May-2019 23:22:01 Sending build context to Docker daemon 281.1kB build 30-May-2019 23:22:01 build 30-May-2019 23:22:01 Step 1/9 : FROM ubuntu:16.04 build 30-May-2019 23:22:01 ---> 2a697363a870 build 30-May-2019 23:22:01 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 30-May-2019 23:22:01 ---> Running in 6964302c334e build 30-May-2019 23:22:02 Removing intermediate container 6964302c334e build 30-May-2019 23:22:02 ---> 07339c96c1a7 build 30-May-2019 23:22:02 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 30-May-2019 23:22:02 ---> Running in e1d55c285641 build 30-May-2019 23:22:08 Reading package lists... build 30-May-2019 23:22:08 Building dependency tree... build 30-May-2019 23:22:08 Reading state information... build 30-May-2019 23:22:08 The following additional packages will be installed: build 30-May-2019 23:22:08 ca-certificates libexpat1 libffi6 libpython-stdlib libpython2.7-minimal build 30-May-2019 23:22:08 libpython2.7-stdlib libsqlite3-0 libssl1.0.0 mime-support openssl build 30-May-2019 23:22:08 python-minimal python-pip-whl python2.7 python2.7-minimal build 30-May-2019 23:22:08 Suggested packages: build 30-May-2019 23:22:08 python-doc python-tk python2.7-doc binutils binfmt-support build 30-May-2019 23:22:08 Recommended packages: build 30-May-2019 23:22:08 file build-essential python-all-dev python-setuptools python-wheel build 30-May-2019 23:22:08 The following NEW packages will be installed: build 30-May-2019 23:22:08 ca-certificates libexpat1 libffi6 libpython-stdlib libpython2.7-minimal build 30-May-2019 23:22:08 libpython2.7-stdlib libsqlite3-0 libssl1.0.0 mime-support openssl python build 30-May-2019 23:22:08 python-minimal python-pip python-pip-whl python2.7 python2.7-minimal build 30-May-2019 23:22:09 0 upgraded, 16 newly installed, 0 to remove and 11 not upgraded. build 30-May-2019 23:22:09 Need to get 7391 kB of archives. build 30-May-2019 23:22:09 After this operation, 24.8 MB of additional disk space will be used. build 30-May-2019 23:22:09 Get:1 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpython2.7-minimal amd64 2.7.12-1ubuntu0~16.04.4 [339 kB] build 30-May-2019 23:22:10 Get:2 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python2.7-minimal amd64 2.7.12-1ubuntu0~16.04.4 [1261 kB] build 30-May-2019 23:22:10 Get:3 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-minimal amd64 2.7.12-1~16.04 [28.1 kB] build 30-May-2019 23:22:10 Get:4 http://archive.ubuntu.com/ubuntu xenial/main amd64 mime-support all 3.59ubuntu1 [31.0 kB] build 30-May-2019 23:22:10 Get:5 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libexpat1 amd64 2.1.0-7ubuntu0.16.04.3 [71.2 kB] build 30-May-2019 23:22:10 Get:6 http://archive.ubuntu.com/ubuntu xenial/main amd64 libffi6 amd64 3.2.1-4 [17.8 kB] build 30-May-2019 23:22:10 Get:7 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libsqlite3-0 amd64 3.11.0-1ubuntu1.1 [396 kB] build 30-May-2019 23:22:10 Get:8 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libssl1.0.0 amd64 1.0.2g-1ubuntu4.15 [1084 kB] build 30-May-2019 23:22:10 Get:9 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpython2.7-stdlib amd64 2.7.12-1ubuntu0~16.04.4 [1880 kB] build 30-May-2019 23:22:10 Get:10 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python2.7 amd64 2.7.12-1ubuntu0~16.04.4 [224 kB] build 30-May-2019 23:22:10 Get:11 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpython-stdlib amd64 2.7.12-1~16.04 [7768 B] build 30-May-2019 23:22:10 Get:12 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 python amd64 2.7.12-1~16.04 [137 kB] build 30-May-2019 23:22:10 Get:13 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 openssl amd64 1.0.2g-1ubuntu4.15 [492 kB] build 30-May-2019 23:22:10 Get:14 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 ca-certificates all 20170717~16.04.2 [167 kB] build 30-May-2019 23:22:10 Get:15 http://archive.ubuntu.com/ubuntu xenial-updates/universe amd64 python-pip-whl all 8.1.1-2ubuntu0.4 [1110 kB] build 30-May-2019 23:22:10 Get:16 http://archive.ubuntu.com/ubuntu xenial-updates/universe amd64 python-pip all 8.1.1-2ubuntu0.4 [144 kB] build 30-May-2019 23:22:11 debconf: delaying package configuration, since apt-utils is not installed build 30-May-2019 23:22:11 Fetched 7391 kB in 1s (4452 kB/s) build 30-May-2019 23:22:11 Selecting previously unselected package libpython2.7-minimal:amd64. build 30-May-2019 23:22:11 (Reading database ... build 30-May-2019 23:22:11 (Reading database ... 5% build 30-May-2019 23:22:11 (Reading database ... 10% build 30-May-2019 23:22:11 (Reading database ... 15% build 30-May-2019 23:22:11 (Reading database ... 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.../libpython2.7-minimal_2.7.12-1ubuntu0~16.04.4_amd64.deb ... build 30-May-2019 23:22:11 Unpacking libpython2.7-minimal:amd64 (2.7.12-1ubuntu0~16.04.4) ... build 30-May-2019 23:22:12 Selecting previously unselected package python2.7-minimal. build 30-May-2019 23:22:12 Preparing to unpack .../python2.7-minimal_2.7.12-1ubuntu0~16.04.4_amd64.deb ... build 30-May-2019 23:22:12 Unpacking python2.7-minimal (2.7.12-1ubuntu0~16.04.4) ... build 30-May-2019 23:22:13 Selecting previously unselected package python-minimal. build 30-May-2019 23:22:13 Preparing to unpack .../python-minimal_2.7.12-1~16.04_amd64.deb ... build 30-May-2019 23:22:13 Unpacking python-minimal (2.7.12-1~16.04) ... build 30-May-2019 23:22:14 Selecting previously unselected package mime-support. build 30-May-2019 23:22:14 Preparing to unpack .../mime-support_3.59ubuntu1_all.deb ... build 30-May-2019 23:22:14 Unpacking mime-support (3.59ubuntu1) ... build 30-May-2019 23:22:14 Selecting previously unselected package libexpat1:amd64. build 30-May-2019 23:22:14 Preparing to unpack .../libexpat1_2.1.0-7ubuntu0.16.04.3_amd64.deb ... build 30-May-2019 23:22:14 Unpacking libexpat1:amd64 (2.1.0-7ubuntu0.16.04.3) ... build 30-May-2019 23:22:15 Selecting previously unselected package libffi6:amd64. build 30-May-2019 23:22:15 Preparing to unpack .../libffi6_3.2.1-4_amd64.deb ... build 30-May-2019 23:22:15 Unpacking libffi6:amd64 (3.2.1-4) ... build 30-May-2019 23:22:15 Selecting previously unselected package libsqlite3-0:amd64. build 30-May-2019 23:22:15 Preparing to unpack .../libsqlite3-0_3.11.0-1ubuntu1.1_amd64.deb ... build 30-May-2019 23:22:15 Unpacking libsqlite3-0:amd64 (3.11.0-1ubuntu1.1) ... build 30-May-2019 23:22:15 Selecting previously unselected package libssl1.0.0:amd64. build 30-May-2019 23:22:15 Preparing to unpack .../libssl1.0.0_1.0.2g-1ubuntu4.15_amd64.deb ... build 30-May-2019 23:22:15 Unpacking libssl1.0.0:amd64 (1.0.2g-1ubuntu4.15) ... build 30-May-2019 23:22:16 Selecting previously unselected package libpython2.7-stdlib:amd64. build 30-May-2019 23:22:16 Preparing to unpack .../libpython2.7-stdlib_2.7.12-1ubuntu0~16.04.4_amd64.deb ... build 30-May-2019 23:22:16 Unpacking libpython2.7-stdlib:amd64 (2.7.12-1ubuntu0~16.04.4) ... build 30-May-2019 23:22:17 Selecting previously unselected package python2.7. build 30-May-2019 23:22:17 Preparing to unpack .../python2.7_2.7.12-1ubuntu0~16.04.4_amd64.deb ... build 30-May-2019 23:22:17 Unpacking python2.7 (2.7.12-1ubuntu0~16.04.4) ... build 30-May-2019 23:22:18 Selecting previously unselected package libpython-stdlib:amd64. build 30-May-2019 23:22:18 Preparing to unpack .../libpython-stdlib_2.7.12-1~16.04_amd64.deb ... build 30-May-2019 23:22:18 Unpacking libpython-stdlib:amd64 (2.7.12-1~16.04) ... build 30-May-2019 23:22:18 Processing triggers for libc-bin (2.23-0ubuntu11) ... build 30-May-2019 23:22:18 Setting up libpython2.7-minimal:amd64 (2.7.12-1ubuntu0~16.04.4) ... build 30-May-2019 23:22:19 Setting up python2.7-minimal (2.7.12-1ubuntu0~16.04.4) ... build 30-May-2019 23:22:19 Linking and byte-compiling packages for runtime python2.7... build 30-May-2019 23:22:19 Setting up python-minimal (2.7.12-1~16.04) ... build 30-May-2019 23:22:20 Selecting previously unselected package python. build 30-May-2019 23:22:20 (Reading database ... build 30-May-2019 23:22:20 (Reading database ... 5% build 30-May-2019 23:22:20 (Reading database ... 10% build 30-May-2019 23:22:20 (Reading database ... 15% build 30-May-2019 23:22:20 (Reading database ... 20% build 30-May-2019 23:22:20 (Reading database ... 25% build 30-May-2019 23:22:20 (Reading database ... 30% build 30-May-2019 23:22:20 (Reading database ... 35% build 30-May-2019 23:22:20 (Reading database ... 40% build 30-May-2019 23:22:20 (Reading database ... 45% build 30-May-2019 23:22:20 (Reading database ... 50% build 30-May-2019 23:22:20 (Reading database ... 55% build 30-May-2019 23:22:20 (Reading database ... 60% build 30-May-2019 23:22:20 (Reading database ... 65% build 30-May-2019 23:22:20 (Reading database ... 70% build 30-May-2019 23:22:20 (Reading database ... 75% build 30-May-2019 23:22:20 (Reading database ... 80% build 30-May-2019 23:22:20 (Reading database ... 85% build 30-May-2019 23:22:20 (Reading database ... 90% build 30-May-2019 23:22:20 (Reading database ... 95% build 30-May-2019 23:22:20 (Reading database ... 100% build 30-May-2019 23:22:20 (Reading database ... 5588 files and directories currently installed.) build 30-May-2019 23:22:20 Preparing to unpack .../python_2.7.12-1~16.04_amd64.deb ... build 30-May-2019 23:22:20 Unpacking python (2.7.12-1~16.04) ... build 30-May-2019 23:22:21 Selecting previously unselected package openssl. build 30-May-2019 23:22:21 Preparing to unpack .../openssl_1.0.2g-1ubuntu4.15_amd64.deb ... build 30-May-2019 23:22:21 Unpacking openssl (1.0.2g-1ubuntu4.15) ... build 30-May-2019 23:22:21 Selecting previously unselected package ca-certificates. build 30-May-2019 23:22:21 Preparing to unpack .../ca-certificates_20170717~16.04.2_all.deb ... build 30-May-2019 23:22:22 Unpacking ca-certificates (20170717~16.04.2) ... build 30-May-2019 23:22:22 Selecting previously unselected package python-pip-whl. build 30-May-2019 23:22:22 Preparing to unpack .../python-pip-whl_8.1.1-2ubuntu0.4_all.deb ... build 30-May-2019 23:22:22 Unpacking python-pip-whl (8.1.1-2ubuntu0.4) ... build 30-May-2019 23:22:22 Selecting previously unselected package python-pip. build 30-May-2019 23:22:22 Preparing to unpack .../python-pip_8.1.1-2ubuntu0.4_all.deb ... build 30-May-2019 23:22:23 Unpacking python-pip (8.1.1-2ubuntu0.4) ... build 30-May-2019 23:22:23 Setting up mime-support (3.59ubuntu1) ... build 30-May-2019 23:22:23 Setting up libexpat1:amd64 (2.1.0-7ubuntu0.16.04.3) ... build 30-May-2019 23:22:23 Setting up libffi6:amd64 (3.2.1-4) ... build 30-May-2019 23:22:23 Setting up libsqlite3-0:amd64 (3.11.0-1ubuntu1.1) ... build 30-May-2019 23:22:24 Setting up libssl1.0.0:amd64 (1.0.2g-1ubuntu4.15) ... build 30-May-2019 23:22:24 debconf: unable to initialize frontend: Dialog build 30-May-2019 23:22:24 debconf: (TERM is not set, so the dialog frontend is not usable.) build 30-May-2019 23:22:24 debconf: falling back to frontend: Readline build 30-May-2019 23:22:24 debconf: unable to initialize frontend: Readline build 30-May-2019 23:22:24 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 30-May-2019 23:22:24 debconf: falling back to frontend: Teletype build 30-May-2019 23:22:24 Setting up libpython2.7-stdlib:amd64 (2.7.12-1ubuntu0~16.04.4) ... build 30-May-2019 23:22:24 Setting up python2.7 (2.7.12-1ubuntu0~16.04.4) ... build 30-May-2019 23:22:25 Setting up libpython-stdlib:amd64 (2.7.12-1~16.04) ... build 30-May-2019 23:22:26 Setting up python (2.7.12-1~16.04) ... build 30-May-2019 23:22:26 Setting up openssl (1.0.2g-1ubuntu4.15) ... build 30-May-2019 23:22:26 Setting up ca-certificates (20170717~16.04.2) ... build 30-May-2019 23:22:27 debconf: unable to initialize frontend: Dialog build 30-May-2019 23:22:27 debconf: (TERM is not set, so the dialog frontend is not usable.) build 30-May-2019 23:22:27 debconf: falling back to frontend: Readline build 30-May-2019 23:22:27 debconf: unable to initialize frontend: Readline build 30-May-2019 23:22:27 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 30-May-2019 23:22:27 debconf: falling back to frontend: Teletype build 30-May-2019 23:22:27 Setting up python-pip-whl (8.1.1-2ubuntu0.4) ... build 30-May-2019 23:22:27 Setting up python-pip (8.1.1-2ubuntu0.4) ... build 30-May-2019 23:22:29 Processing triggers for libc-bin (2.23-0ubuntu11) ... build 30-May-2019 23:22:29 Processing triggers for ca-certificates (20170717~16.04.2) ... build 30-May-2019 23:22:29 Updating certificates in /etc/ssl/certs... build 30-May-2019 23:22:30 148 added, 0 removed; done. build 30-May-2019 23:22:30 Running hooks in /etc/ca-certificates/update.d... build 30-May-2019 23:22:30 done. build 30-May-2019 23:22:31 Collecting setuptools build 30-May-2019 23:22:32 Downloading https://files.pythonhosted.org/packages/ec/51/f45cea425fd5cb0b0380f5b0f048ebc1da5b417e48d304838c02d6288a1e/setuptools-41.0.1-py2.py3-none-any.whl (575kB) build 30-May-2019 23:22:32 Installing collected packages: setuptools build 30-May-2019 23:22:32 Successfully installed setuptools-41.0.1 build 30-May-2019 23:22:32 You are using pip version 8.1.1, however version 19.1.1 is available. build 30-May-2019 23:22:32 You should consider upgrading via the 'pip install --upgrade pip' command. build 30-May-2019 23:22:34 Removing intermediate container e1d55c285641 build 30-May-2019 23:22:34 ---> 66b8b13e8095 build 30-May-2019 23:22:34 Step 4/9 : COPY pyclowder /tmp/pyclowder/pyclowder build 30-May-2019 23:22:34 ---> d8c1b0c331b0 build 30-May-2019 23:22:34 Step 5/9 : COPY setup.py description.rst /tmp/pyclowder/ build 30-May-2019 23:22:35 ---> 53f00a224aaa build 30-May-2019 23:22:35 Step 6/9 : RUN pip install --upgrade /tmp/pyclowder && rm -rf /tmp/pyclowder build 30-May-2019 23:22:36 ---> Running in b307c47b6018 build 30-May-2019 23:22:37 Processing /tmp/pyclowder build 30-May-2019 23:22:37 Collecting enum34==1.1.6 (from pyclowder===2.1.1) build 30-May-2019 23:22:37 Downloading https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl build 30-May-2019 23:22:37 Collecting pika==1.0.0 (from pyclowder===2.1.1) build 30-May-2019 23:22:38 Downloading https://files.pythonhosted.org/packages/53/a4/5aff2293e1cdcf5f77447ebdfeaac99b622aef7d1e723cf9a5fe317b077c/pika-1.0.0-py2.py3-none-any.whl (148kB) build 30-May-2019 23:22:38 Collecting PyYAML==5.1 (from pyclowder===2.1.1) build 30-May-2019 23:22:38 Downloading https://files.pythonhosted.org/packages/9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d/PyYAML-5.1.tar.gz (274kB) build 30-May-2019 23:22:38 Collecting requests==2.21.0 (from pyclowder===2.1.1) build 30-May-2019 23:22:38 Downloading https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl (57kB) build 30-May-2019 23:22:38 Collecting certifi>=2017.4.17 (from requests==2.21.0->pyclowder===2.1.1) build 30-May-2019 23:22:38 Downloading https://files.pythonhosted.org/packages/60/75/f692a584e85b7eaba0e03827b3d51f45f571c2e793dd731e598828d380aa/certifi-2019.3.9-py2.py3-none-any.whl (158kB) build 30-May-2019 23:22:38 Collecting chardet<3.1.0,>=3.0.2 (from requests==2.21.0->pyclowder===2.1.1) build 30-May-2019 23:22:38 Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB) build 30-May-2019 23:22:38 Collecting idna<2.9,>=2.5 (from requests==2.21.0->pyclowder===2.1.1) build 30-May-2019 23:22:38 Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB) build 30-May-2019 23:22:38 Collecting urllib3<1.25,>=1.21.1 (from requests==2.21.0->pyclowder===2.1.1) build 30-May-2019 23:22:38 Downloading https://files.pythonhosted.org/packages/01/11/525b02e4acc0c747de8b6ccdab376331597c569c42ea66ab0a1dbd36eca2/urllib3-1.24.3-py2.py3-none-any.whl (118kB) build 30-May-2019 23:22:38 Building wheels for collected packages: PyYAML build 30-May-2019 23:22:38 Running setup.py bdist_wheel for PyYAML: started build 30-May-2019 23:22:39 Running setup.py bdist_wheel for PyYAML: finished with status 'error' build 30-May-2019 23:22:39 Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-1e0Tf6/PyYAML/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /tmp/tmpJhpxPEpip-wheel- --python-tag cp27: build 30-May-2019 23:22:39 usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] build 30-May-2019 23:22:39 or: -c --help [cmd1 cmd2 ...] build 30-May-2019 23:22:39 or: -c --help-commands build 30-May-2019 23:22:39 or: -c cmd --help build 30-May-2019 23:22:39 build 30-May-2019 23:22:39 error: invalid command 'bdist_wheel' build 30-May-2019 23:22:39 build 30-May-2019 23:22:39 ---------------------------------------- build 30-May-2019 23:22:39  Failed building wheel for PyYAML build 30-May-2019 23:22:39  Running setup.py clean for PyYAML build 30-May-2019 23:22:39 Failed to build PyYAML build 30-May-2019 23:22:39 Installing collected packages: enum34, pika, PyYAML, certifi, chardet, idna, urllib3, requests, pyclowder build 30-May-2019 23:22:39 Running setup.py install for PyYAML: started build 30-May-2019 23:22:39 Running setup.py install for PyYAML: finished with status 'done' build 30-May-2019 23:22:39 Running setup.py install for pyclowder: started build 30-May-2019 23:22:40 Running setup.py install for pyclowder: finished with status 'done' build 30-May-2019 23:22:40 Successfully installed PyYAML-5.1 certifi-2019.3.9 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 30-May-2019 23:22:40 You are using pip version 8.1.1, however version 19.1.1 is available. build 30-May-2019 23:22:40 You should consider upgrading via the 'pip install --upgrade pip' command. build 30-May-2019 23:22:41 Removing intermediate container b307c47b6018 build 30-May-2019 23:22:41 ---> eee101981043 build 30-May-2019 23:22:41 Step 7/9 : WORKDIR /home/clowder build 30-May-2019 23:22:42 ---> Running in 8d2594a5ba62 build 30-May-2019 23:22:42 Removing intermediate container 8d2594a5ba62 build 30-May-2019 23:22:42 ---> c91f4b8f86bc build 30-May-2019 23:22:42 Step 8/9 : COPY notifications.json /home/clowder build 30-May-2019 23:22:43 ---> dbc4c8fabc3a build 30-May-2019 23:22:43 Step 9/9 : CMD python "./${MAIN_SCRIPT}" build 30-May-2019 23:22:43 ---> Running in a970fcb0a3fc build 30-May-2019 23:22:43 Removing intermediate container a970fcb0a3fc build 30-May-2019 23:22:43 ---> e3941ef228e0 build 30-May-2019 23:22:43 Successfully built e3941ef228e0 build 30-May-2019 23:22:43 Successfully tagged clowder/pyclowder:latest build 30-May-2019 23:22:43 Sending build context to Docker daemon 279.6kB build 30-May-2019 23:22:43 build 30-May-2019 23:22:43 Step 1/6 : FROM clowder/pyclowder build 30-May-2019 23:22:43 ---> e3941ef228e0 build 30-May-2019 23:22:43 Step 2/6 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:22:44 ---> Running in d839e107ddaf build 30-May-2019 23:22:44 Removing intermediate container d839e107ddaf build 30-May-2019 23:22:44 ---> b373d4266138 build 30-May-2019 23:22:44 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 30-May-2019 23:22:44 ---> Running in 0fd90c2fd88a build 30-May-2019 23:22:44 Removing intermediate container 0fd90c2fd88a build 30-May-2019 23:22:44 ---> 8fd45ef39137 build 30-May-2019 23:22:44 Step 4/6 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 30-May-2019 23:22:45 ---> Running in 4dfa54c45146 build 30-May-2019 23:22:45 Removing intermediate container 4dfa54c45146 build 30-May-2019 23:22:45 ---> c483dc4e92f2 build 30-May-2019 23:22:45 Step 5/6 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 30-May-2019 23:22:45 ---> Running in d841eca52e2f build 30-May-2019 23:22:45 Removing intermediate container d841eca52e2f build 30-May-2019 23:22:45 ---> d19ae6315361 build 30-May-2019 23:22:45 Step 6/6 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:22:46 ---> Running in c54749988bd7 build 30-May-2019 23:22:46 Removing intermediate container c54749988bd7 build 30-May-2019 23:22:46 ---> 826af52f4fb4 build 30-May-2019 23:22:46 Successfully built 826af52f4fb4 build 30-May-2019 23:22:46 Successfully tagged clowder/pyclowder:onbuild build 30-May-2019 23:22:47 Sending build context to Docker daemon 12.8kB build 30-May-2019 23:22:47 build 30-May-2019 23:22:47 Step 1/5 : FROM clowder/pyclowder:onbuild build 30-May-2019 23:22:47 # Executing 5 build triggers build 30-May-2019 23:22:47 ---> Running in aadc85c8ba47 build 30-May-2019 23:22:49 Removing intermediate container aadc85c8ba47 build 30-May-2019 23:22:50 ---> Running in f4fdb08a1754 build 30-May-2019 23:22:52 Removing intermediate container f4fdb08a1754 build 30-May-2019 23:22:52 ---> 1b2b7fc9f69e build 30-May-2019 23:22:52 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 30-May-2019 23:22:52 ---> Running in 44bd32e5f959 build 30-May-2019 23:22:53 Removing intermediate container 44bd32e5f959 build 30-May-2019 23:22:53 ---> 24756082800c build 30-May-2019 23:22:53 Step 3/5 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:22:53 ---> Running in ee910cb9a67e build 30-May-2019 23:22:53 Removing intermediate container ee910cb9a67e build 30-May-2019 23:22:53 ---> f536f83844cf build 30-May-2019 23:22:53 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 30-May-2019 23:22:53 ---> Running in cebf728d86d7 build 30-May-2019 23:22:54 Removing intermediate container cebf728d86d7 build 30-May-2019 23:22:54 ---> e26084fcad02 build 30-May-2019 23:22:54 Step 5/5 : ONBUILD COPY extractor_info.json /home/clowder/ build 30-May-2019 23:22:54 ---> Running in 6e93b76b9cc7 build 30-May-2019 23:22:55 Removing intermediate container 6e93b76b9cc7 build 30-May-2019 23:22:55 ---> 2dfbb5176899 build 30-May-2019 23:22:55 Successfully built 2dfbb5176899 build 30-May-2019 23:22:55 Successfully tagged clowder/extractors-binary-preview:onbuild build 30-May-2019 23:22:55 Sending build context to Docker daemon 6.656kB build 30-May-2019 23:22:55 build 30-May-2019 23:22:55 Step 1/9 : FROM clowder/pyclowder:onbuild build 30-May-2019 23:22:55 # Executing 5 build triggers build 30-May-2019 23:22:56 ---> Running in 66a4a9bd7d56 build 30-May-2019 23:22:57 Removing intermediate container 66a4a9bd7d56 build 30-May-2019 23:22:58 ---> Running in c72f290eeba9 build 30-May-2019 23:22:59 Removing intermediate container c72f290eeba9 build 30-May-2019 23:23:00 ---> 86ff6d69b221 build 30-May-2019 23:23:00 Step 2/9 : ENV EXTRACTION_FUNC="" build 30-May-2019 23:23:00 ---> Running in 6ba040c0eaf8 build 30-May-2019 23:23:01 Removing intermediate container 6ba040c0eaf8 build 30-May-2019 23:23:01 ---> af366a91ccdd build 30-May-2019 23:23:01 Step 3/9 : ENV EXTRACTION_MODULE="" build 30-May-2019 23:23:01 ---> Running in d4fbc8ec5842 build 30-May-2019 23:23:01 Removing intermediate container d4fbc8ec5842 build 30-May-2019 23:23:01 ---> 5ccb678d30c6 build 30-May-2019 23:23:01 Step 4/9 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:23:01 ---> Running in 1be0fbb8fa90 build 30-May-2019 23:23:02 Removing intermediate container 1be0fbb8fa90 build 30-May-2019 23:23:02 ---> 5508388d0713 build 30-May-2019 23:23:02 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 30-May-2019 23:23:02 ---> Running in 94c92a337ccc build 30-May-2019 23:23:02 Removing intermediate container 94c92a337ccc build 30-May-2019 23:23:02 ---> a015d01ce7f7 build 30-May-2019 23:23:02 Step 6/9 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 30-May-2019 23:23:02 ---> Running in b778377ca0f7 build 30-May-2019 23:23:03 Removing intermediate container b778377ca0f7 build 30-May-2019 23:23:03 ---> 55cac8451e2f build 30-May-2019 23:23:03 Step 7/9 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 30-May-2019 23:23:03 ---> Running in 6ebb639def30 build 30-May-2019 23:23:03 Removing intermediate container 6ebb639def30 build 30-May-2019 23:23:03 ---> 508f78486461 build 30-May-2019 23:23:03 Step 8/9 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:23:03 ---> Running in 174272c6b500 build 30-May-2019 23:23:04 Removing intermediate container 174272c6b500 build 30-May-2019 23:23:04 ---> f5d1282df646 build 30-May-2019 23:23:04 Step 9/9 : CMD python -c "from simple_extractor import SimplePythonExtractor; from ${EXTRACTION_MODULE} import *; SimplePythonExtractor(${EXTRACTION_FUNC}).start()" build 30-May-2019 23:23:04 ---> Running in 7114840328e0 build 30-May-2019 23:23:04 Removing intermediate container 7114840328e0 build 30-May-2019 23:23:04 ---> c6fdc7456e56 build 30-May-2019 23:23:04 Successfully built c6fdc7456e56 build 30-May-2019 23:23:04 Successfully tagged clowder/extractors-simple-extractor:onbuild build 30-May-2019 23:23:04 Sending build context to Docker daemon 13.31kB build 30-May-2019 23:23:04 build 30-May-2019 23:23:04 Step 1/10 : FROM clowder/pyclowder:latest build 30-May-2019 23:23:04 ---> e3941ef228e0 build 30-May-2019 23:23:04 Step 2/10 : ENV R_SCRIPT="" R_FUNCTION="" build 30-May-2019 23:23:05 ---> Running in c28cb313e14c build 30-May-2019 23:23:06 Removing intermediate container c28cb313e14c build 30-May-2019 23:23:06 ---> 4b8f93c5517d build 30-May-2019 23:23:06 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 30-May-2019 23:23:06 ---> Running in 6e66337cf6c5 build 30-May-2019 23:23:07 Executing: /tmp/tmp.Cm9d2dwL1F/gpg.1.sh --keyserver build 30-May-2019 23:23:07 keyserver.ubuntu.com build 30-May-2019 23:23:07 --recv build 30-May-2019 23:23:07 E084DAB9 build 30-May-2019 23:23:07 gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com build 30-May-2019 23:23:08 gpg: key E084DAB9: public key "Totally Legit Signing Key " imported build 30-May-2019 23:23:08 gpg: key E084DAB9: public key "Michael Rutter " imported build 30-May-2019 23:23:08 gpg: Total number processed: 2 build 30-May-2019 23:23:08 gpg:  imported: 2 (RSA: 2) build 30-May-2019 23:23:26 Reading package lists... build 30-May-2019 23:23:26 Building dependency tree... build 30-May-2019 23:23:26 Reading state information... build 30-May-2019 23:23:27 The following additional packages will be installed: build 30-May-2019 23:23:27 autoconf automake autotools-dev binutils bsdmainutils build-essential bzip2 build 30-May-2019 23:23:27 cdbs cpp cpp-5 debhelper dh-strip-nondeterminism dh-translations dpkg-dev build 30-May-2019 23:23:27 file fontconfig fontconfig-config fonts-dejavu-core g++ g++-5 gcc gcc-5 build 30-May-2019 23:23:27 gettext gettext-base gfortran gfortran-5 groff-base icu-devtools intltool build 30-May-2019 23:23:27 intltool-debian libarchive-zip-perl libasan2 libasn1-8-heimdal build 30-May-2019 23:23:27 libasprintf0v5 libatomic1 libblas-common libblas-dev libblas3 libbz2-dev build 30-May-2019 23:23:27 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcilkrts5 libcroco3 libcurl3 build 30-May-2019 23:23:27 libdatrie1 libdpkg-perl libencode-locale-perl libfile-listing-perl build 30-May-2019 23:23:27 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-5-dev build 30-May-2019 23:23:27 libgdbm3 libgfortran-5-dev libgfortran3 libglib2.0-0 libgmp10 libgnutls30 build 30-May-2019 23:23:27 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b build 30-May-2019 23:23:27 libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 build 30-May-2019 23:23:27 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl build 30-May-2019 23:23:27 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl build 30-May-2019 23:23:27 libhttp-negotiate-perl libhx509-5-heimdal libice6 libicu-dev libicu55 build 30-May-2019 23:23:27 libidn11 libio-html-perl libio-socket-ssl-perl libisl15 libitm1 libjbig0 build 30-May-2019 23:23:27 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev build 30-May-2019 23:23:27 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 build 30-May-2019 23:23:27 liblapack-dev liblapack3 libldap-2.4-2 liblsan0 liblwp-mediatypes-perl build 30-May-2019 23:23:27 liblwp-protocol-https-perl liblzma-dev libmagic1 libmpc3 libmpfr4 libmpx0 build 30-May-2019 23:23:27 libncurses5-dev libnet-http-perl libnet-ssleay-perl libnettle6 libp11-kit0 build 30-May-2019 23:23:27 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils build 30-May-2019 23:23:27 libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libperl5.22 build 30-May-2019 23:23:27 libpipeline1 libpixman-1-0 libpng12-0 libpng12-dev libquadmath0 build 30-May-2019 23:23:27 libreadline-dev libreadline6-dev libroken18-heimdal librtmp1 libsasl2-2 build 30-May-2019 23:23:27 libsasl2-modules-db libsigsegv2 libsm6 libstdc++-5-dev libtasn1-6 libtcl8.6 build 30-May-2019 23:23:27 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 build 30-May-2019 23:23:27 libtsan0 libubsan0 libunistring0 liburi-perl libwind0-heimdal libwww-perl build 30-May-2019 23:23:27 libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 build 30-May-2019 23:23:27 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml2 build 30-May-2019 23:23:27 libxmuu1 libxrender1 libxss1 libxt6 linux-libc-dev m4 make man-db netbase build 30-May-2019 23:23:27 patch perl perl-modules-5.22 pkg-config po-debconf python-pkg-resources build 30-May-2019 23:23:27 python-scour python-six tzdata ucf unzip x11-common xauth xdg-utils xz-utils build 30-May-2019 23:23:27 zip zlib1g-dev build 30-May-2019 23:23:27 Suggested packages: build 30-May-2019 23:23:27 autoconf-archive gnu-standards autoconf-doc libtool binutils-doc wamerican build 30-May-2019 23:23:27 | wordlist whois vacation bzip2-doc devscripts cpp-doc gcc-5-locales dh-make build 30-May-2019 23:23:27 debian-keyring g++-multilib g++-5-multilib gcc-5-doc libstdc++6-5-dbg build 30-May-2019 23:23:27 gcc-multilib manpages-dev flex bison gdb gcc-doc gcc-5-multilib libgcc1-dbg build 30-May-2019 23:23:27 libgomp1-dbg libitm1-dbg libatomic1-dbg libasan2-dbg liblsan0-dbg build 30-May-2019 23:23:27 libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx0-dbg libquadmath0-dbg build 30-May-2019 23:23:27 gettext-doc autopoint gfortran-multilib gfortran-doc gfortran-5-multilib build 30-May-2019 23:23:27 gfortran-5-doc libgfortran3-dbg groff liblapack-doc-man liblapack-doc build 30-May-2019 23:23:27 glibc-doc gnutls-bin krb5-doc krb5-user libdata-dump-perl icu-doc build 30-May-2019 23:23:27 libcrypt-ssleay-perl liblzma-doc ncurses-doc readline-doc libstdc++-5-doc build 30-May-2019 23:23:27 tcl8.6 tk8.6 libauthen-ntlm-perl make-doc less www-browser ed diffutils-doc build 30-May-2019 23:23:27 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl build 30-May-2019 23:23:27 libmail-box-perl python-setuptools python-rsvg python-cairo ess r-doc-info build 30-May-2019 23:23:27 | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base build 30-May-2019 23:23:27 texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra build 30-May-2019 23:23:27 texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo build 30-May-2019 23:23:27 gvfs-bin build 30-May-2019 23:23:27 Recommended packages: build 30-May-2019 23:23:27 fakeroot libalgorithm-merge-perl curl | wget | lynx-cur libasprintf-dev build 30-May-2019 23:23:27 libgettextpo-dev bzip2-doc manpages manpages-dev libfile-fcntllock-perl build 30-May-2019 23:23:27 libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl build 30-May-2019 23:23:27 krb5-locales libsasl2-modules libhtml-form-perl libhttp-daemon-perl build 30-May-2019 23:23:27 libmailtools-perl xml-core ifupdown rename libmail-sendmail-perl build 30-May-2019 23:23:27 r-recommended r-doc-html libfile-mimeinfo-perl libnet-dbus-perl build 30-May-2019 23:23:27 libx11-protocol-perl x11-utils x11-xserver-utils build 30-May-2019 23:23:27 The following NEW packages will be installed: build 30-May-2019 23:23:27 autoconf automake autotools-dev binutils bsdmainutils build-essential bzip2 build 30-May-2019 23:23:27 cdbs cpp cpp-5 debhelper dh-strip-nondeterminism dh-translations dpkg-dev build 30-May-2019 23:23:27 file fontconfig fontconfig-config fonts-dejavu-core g++ g++-5 gcc gcc-5 build 30-May-2019 23:23:27 gettext gettext-base gfortran gfortran-5 groff-base icu-devtools intltool build 30-May-2019 23:23:27 intltool-debian libarchive-zip-perl libasan2 libasn1-8-heimdal build 30-May-2019 23:23:27 libasprintf0v5 libatomic1 libblas-common libblas-dev libblas3 libbz2-dev build 30-May-2019 23:23:27 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcilkrts5 libcroco3 libcurl3 build 30-May-2019 23:23:27 libdatrie1 libdpkg-perl libencode-locale-perl libfile-listing-perl build 30-May-2019 23:23:27 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-5-dev build 30-May-2019 23:23:27 libgdbm3 libgfortran-5-dev libgfortran3 libglib2.0-0 libgmp10 libgnutls30 build 30-May-2019 23:23:27 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b build 30-May-2019 23:23:27 libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 build 30-May-2019 23:23:27 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl build 30-May-2019 23:23:27 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl build 30-May-2019 23:23:27 libhttp-negotiate-perl libhx509-5-heimdal libice6 libicu-dev libicu55 build 30-May-2019 23:23:27 libidn11 libio-html-perl libio-socket-ssl-perl libisl15 libitm1 libjbig0 build 30-May-2019 23:23:27 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev build 30-May-2019 23:23:27 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 build 30-May-2019 23:23:27 liblapack-dev liblapack3 libldap-2.4-2 liblsan0 liblwp-mediatypes-perl build 30-May-2019 23:23:27 liblwp-protocol-https-perl liblzma-dev libmagic1 libmpc3 libmpfr4 libmpx0 build 30-May-2019 23:23:27 libncurses5-dev libnet-http-perl libnet-ssleay-perl libnettle6 libp11-kit0 build 30-May-2019 23:23:27 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils build 30-May-2019 23:23:27 libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libperl5.22 build 30-May-2019 23:23:27 libpipeline1 libpixman-1-0 libpng12-0 libpng12-dev libquadmath0 build 30-May-2019 23:23:27 libreadline-dev libreadline6-dev libroken18-heimdal librtmp1 libsasl2-2 build 30-May-2019 23:23:27 libsasl2-modules-db libsigsegv2 libsm6 libstdc++-5-dev libtasn1-6 libtcl8.6 build 30-May-2019 23:23:27 libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6 build 30-May-2019 23:23:27 libtsan0 libubsan0 libunistring0 liburi-perl libwind0-heimdal libwww-perl build 30-May-2019 23:23:27 libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 build 30-May-2019 23:23:27 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml2 build 30-May-2019 23:23:27 libxmuu1 libxrender1 libxss1 libxt6 linux-libc-dev m4 make man-db netbase build 30-May-2019 23:23:27 patch perl perl-modules-5.22 pkg-config po-debconf python-pkg-resources build 30-May-2019 23:23:27 python-scour python-six r-base-core r-base-dev tzdata ucf unzip x11-common build 30-May-2019 23:23:27 xauth xdg-utils xz-utils zip zlib1g-dev build 30-May-2019 23:23:27 0 upgraded, 190 newly installed, 0 to remove and 11 not upgraded. build 30-May-2019 23:23:27 Need to get 116 MB of archives. build 30-May-2019 23:23:27 After this operation, 416 MB of additional disk space will be used. build 30-May-2019 23:23:27 Get:1 http://cran.rstudio.com/bin/linux/ubuntu xenial/ r-base-core 3.4.4-1xenial0 [23.2 MB] build 30-May-2019 23:23:27 Get:2 http://cran.rstudio.com/bin/linux/ubuntu xenial/ r-base-dev 3.4.4-1xenial0 [4416 B] build 30-May-2019 23:23:27 Get:3 http://archive.ubuntu.com/ubuntu xenial/main amd64 libgdbm3 amd64 1.8.3-13.1 [16.9 kB] build 30-May-2019 23:23:28 Get:4 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libglib2.0-0 amd64 2.48.2-0ubuntu4.1 [1120 kB] build 30-May-2019 23:23:28 Get:5 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B] build 30-May-2019 23:23:28 Get:6 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [11.0 kB] build 30-May-2019 23:23:28 Get:7 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxcb1 amd64 1.11.1-1ubuntu1 [40.0 kB] build 30-May-2019 23:23:28 Get:8 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libx11-data all 2:1.6.3-1ubuntu2.1 [113 kB] build 30-May-2019 23:23:28 Get:9 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libx11-6 amd64 2:1.6.3-1ubuntu2.1 [570 kB] build 30-May-2019 23:23:28 Get:10 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB] build 30-May-2019 23:23:28 Get:11 http://archive.ubuntu.com/ubuntu xenial/main amd64 groff-base amd64 1.22.3-7 [1151 kB] build 30-May-2019 23:23:28 Get:12 http://archive.ubuntu.com/ubuntu xenial/main amd64 bsdmainutils amd64 9.0.6ubuntu3 [174 kB] build 30-May-2019 23:23:28 Get:13 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpipeline1 amd64 1.4.1-2 [24.6 kB] build 30-May-2019 23:23:28 Get:14 http://archive.ubuntu.com/ubuntu xenial/main amd64 man-db amd64 2.7.5-1 [854 kB] build 30-May-2019 23:23:28 Get:15 http://archive.ubuntu.com/ubuntu xenial/main amd64 fonts-dejavu-core all 2.35-1 [1039 kB] build 30-May-2019 23:23:28 Get:16 http://archive.ubuntu.com/ubuntu xenial/main amd64 ucf all 3.0036 [52.9 kB] build 30-May-2019 23:23:28 Get:17 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 fontconfig-config all 2.11.94-0ubuntu1.1 [49.9 kB] build 30-May-2019 23:23:28 Get:18 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpng12-0 amd64 1.2.54-1ubuntu1.1 [116 kB] build 30-May-2019 23:23:28 Get:19 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libfreetype6 amd64 2.6.1-0.1ubuntu2.3 [316 kB] build 30-May-2019 23:23:28 Get:20 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libfontconfig1 amd64 2.11.94-0ubuntu1.1 [131 kB] build 30-May-2019 23:23:28 Get:21 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 fontconfig amd64 2.11.94-0ubuntu1.1 [178 kB] build 30-May-2019 23:23:28 Get:22 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 x11-common all 1:7.7+13ubuntu3.1 [22.9 kB] build 30-May-2019 23:23:28 Get:23 http://archive.ubuntu.com/ubuntu xenial/main amd64 libice6 amd64 2:1.0.9-1 [39.2 kB] build 30-May-2019 23:23:28 Get:24 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libjpeg-turbo8 amd64 1.4.2-0ubuntu3.1 [111 kB] build 30-May-2019 23:23:28 Get:25 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpcrecpp0v5 amd64 2:8.38-3.1 [15.2 kB] build 30-May-2019 23:23:28 Get:26 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsigsegv2 amd64 2.10-4 [14.1 kB] build 30-May-2019 23:23:28 Get:27 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB] build 30-May-2019 23:23:28 Get:28 http://archive.ubuntu.com/ubuntu xenial/main amd64 libunistring0 amd64 0.9.3-5.2ubuntu1 [279 kB] build 30-May-2019 23:23:28 Get:29 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxrender1 amd64 1:0.9.9-0ubuntu1 [18.5 kB] build 30-May-2019 23:23:28 Get:30 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxft2 amd64 2.3.2-1 [36.1 kB] build 30-May-2019 23:23:29 Get:31 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxss1 amd64 1:1.2.2-1 [8582 B] build 30-May-2019 23:23:29 Get:32 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 perl-modules-5.22 all 5.22.1-9ubuntu0.6 [2629 kB] build 30-May-2019 23:23:29 Get:33 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libperl5.22 amd64 5.22.1-9ubuntu0.6 [3405 kB] build 30-May-2019 23:23:29 Get:34 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 perl amd64 5.22.1-9ubuntu0.6 [237 kB] build 30-May-2019 23:23:29 Get:35 http://archive.ubuntu.com/ubuntu xenial/main amd64 libjbig0 amd64 2.1-3.1 [26.6 kB] build 30-May-2019 23:23:29 Get:36 http://archive.ubuntu.com/ubuntu xenial/main amd64 libgmp10 amd64 2:6.1.0+dfsg-2 [240 kB] build 30-May-2019 23:23:29 Get:37 http://archive.ubuntu.com/ubuntu xenial/main amd64 libmpfr4 amd64 3.1.4-1 [191 kB] build 30-May-2019 23:23:29 Get:38 http://archive.ubuntu.com/ubuntu xenial/main amd64 libmpc3 amd64 1.0.3-1 [39.7 kB] build 30-May-2019 23:23:29 Get:39 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 tzdata all 2019a-0ubuntu0.16.04 [167 kB] build 30-May-2019 23:23:29 Get:40 http://archive.ubuntu.com/ubuntu xenial/main amd64 bzip2 amd64 1.0.6-8 [32.7 kB] build 30-May-2019 23:23:29 Get:41 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmagic1 amd64 1:5.25-2ubuntu1.2 [216 kB] build 30-May-2019 23:23:29 Get:42 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 file amd64 1:5.25-2ubuntu1.2 [21.2 kB] build 30-May-2019 23:23:29 Get:43 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libnettle6 amd64 3.2-1ubuntu0.16.04.1 [93.5 kB] build 30-May-2019 23:23:29 Get:44 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libhogweed4 amd64 3.2-1ubuntu0.16.04.1 [136 kB] build 30-May-2019 23:23:29 Get:45 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libidn11 amd64 1.32-3ubuntu1.2 [46.5 kB] build 30-May-2019 23:23:29 Get:46 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libp11-kit0 amd64 0.23.2-5~ubuntu16.04.1 [105 kB] build 30-May-2019 23:23:29 Get:47 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtasn1-6 amd64 4.7-3ubuntu0.16.04.3 [43.5 kB] build 30-May-2019 23:23:29 Get:48 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgnutls30 amd64 3.4.10-4ubuntu1.5 [548 kB] build 30-May-2019 23:23:29 Get:49 http://archive.ubuntu.com/ubuntu xenial/main amd64 netbase all 5.3 [12.9 kB] build 30-May-2019 23:23:29 Get:50 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libasprintf0v5 amd64 0.19.7-2ubuntu3.1 [6568 B] build 30-May-2019 23:23:29 Get:51 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 gettext-base amd64 0.19.7-2ubuntu3.1 [48.0 kB] build 30-May-2019 23:23:29 Get:52 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libroken18-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [41.4 kB] build 30-May-2019 23:23:29 Get:53 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libasn1-8-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [174 kB] build 30-May-2019 23:23:29 Get:54 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkrb5support0 amd64 1.13.2+dfsg-5ubuntu2.1 [31.2 kB] build 30-May-2019 23:23:29 Get:55 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libk5crypto3 amd64 1.13.2+dfsg-5ubuntu2.1 [81.3 kB] build 30-May-2019 23:23:29 Get:56 http://archive.ubuntu.com/ubuntu xenial/main amd64 libkeyutils1 amd64 1.5.9-8ubuntu1 [9904 B] build 30-May-2019 23:23:29 Get:57 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkrb5-3 amd64 1.13.2+dfsg-5ubuntu2.1 [273 kB] build 30-May-2019 23:23:29 Get:58 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgssapi-krb5-2 amd64 1.13.2+dfsg-5ubuntu2.1 [120 kB] build 30-May-2019 23:23:29 Get:59 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libhcrypto4-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [85.0 kB] build 30-May-2019 23:23:29 Get:60 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libheimbase1-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [29.3 kB] build 30-May-2019 23:23:29 Get:61 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libwind0-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [47.8 kB] build 30-May-2019 23:23:29 Get:62 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libhx509-5-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [107 kB] build 30-May-2019 23:23:29 Get:63 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkrb5-26-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [202 kB] build 30-May-2019 23:23:29 Get:64 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libheimntlm0-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [15.1 kB] build 30-May-2019 23:23:29 Get:65 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgssapi3-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1.16.04.1 [96.1 kB] build 30-May-2019 23:23:29 Get:66 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libicu55 amd64 55.1-7ubuntu0.4 [7646 kB] build 30-May-2019 23:23:29 Get:67 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-14ubuntu0.1 [14.5 kB] build 30-May-2019 23:23:29 Get:68 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-14ubuntu0.1 [48.6 kB] build 30-May-2019 23:23:29 Get:69 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2ubuntu3.5 [161 kB] build 30-May-2019 23:23:29 Get:70 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d-1ubuntu0.1 [54.4 kB] build 30-May-2019 23:23:29 Get:71 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libxml2 amd64 2.9.3+dfsg1-1ubuntu0.6 [697 kB] build 30-May-2019 23:23:29 Get:72 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxmuu1 amd64 2:1.1.2-2 [9674 B] build 30-May-2019 23:23:29 Get:73 http://archive.ubuntu.com/ubuntu xenial/main amd64 xauth amd64 1:1.0.9-1ubuntu2 [22.7 kB] build 30-May-2019 23:23:29 Get:74 http://archive.ubuntu.com/ubuntu xenial/main amd64 m4 amd64 1.4.17-5 [195 kB] build 30-May-2019 23:23:29 Get:75 http://archive.ubuntu.com/ubuntu xenial/main amd64 autoconf all 2.69-9 [321 kB] build 30-May-2019 23:23:29 Get:76 http://archive.ubuntu.com/ubuntu xenial/main amd64 autotools-dev all 20150820.1 [39.8 kB] build 30-May-2019 23:23:30 Get:77 http://archive.ubuntu.com/ubuntu xenial/main amd64 automake all 1:1.15-4ubuntu1 [510 kB] build 30-May-2019 23:23:30 Get:78 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 binutils amd64 2.26.1-1ubuntu1~16.04.8 [2312 kB] build 30-May-2019 23:23:30 Get:79 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libc-dev-bin amd64 2.23-0ubuntu11 [68.5 kB] build 30-May-2019 23:23:30 Get:80 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 linux-libc-dev amd64 4.4.0-148.174 [867 kB] build 30-May-2019 23:23:30 Get:81 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libc6-dev amd64 2.23-0ubuntu11 [2086 kB] build 30-May-2019 23:23:30 Get:82 http://archive.ubuntu.com/ubuntu xenial/main amd64 libisl15 amd64 0.16.1-1 [524 kB] build 30-May-2019 23:23:30 Get:83 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 cpp-5 amd64 5.4.0-6ubuntu1~16.04.11 [7660 kB] build 30-May-2019 23:23:30 Get:84 http://archive.ubuntu.com/ubuntu xenial/main amd64 cpp amd64 4:5.3.1-1ubuntu1 [27.7 kB] build 30-May-2019 23:23:30 Get:85 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libcc1-0 amd64 5.4.0-6ubuntu1~16.04.11 [38.8 kB] build 30-May-2019 23:23:30 Get:86 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgomp1 amd64 5.4.0-6ubuntu1~16.04.11 [55.0 kB] build 30-May-2019 23:23:30 Get:87 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libitm1 amd64 5.4.0-6ubuntu1~16.04.11 [27.4 kB] build 30-May-2019 23:23:30 Get:88 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libatomic1 amd64 5.4.0-6ubuntu1~16.04.11 [8896 B] build 30-May-2019 23:23:30 Get:89 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libasan2 amd64 5.4.0-6ubuntu1~16.04.11 [264 kB] build 30-May-2019 23:23:30 Get:90 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 liblsan0 amd64 5.4.0-6ubuntu1~16.04.11 [105 kB] build 30-May-2019 23:23:30 Get:91 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtsan0 amd64 5.4.0-6ubuntu1~16.04.11 [244 kB] build 30-May-2019 23:23:30 Get:92 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libubsan0 amd64 5.4.0-6ubuntu1~16.04.11 [95.4 kB] build 30-May-2019 23:23:30 Get:93 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libcilkrts5 amd64 5.4.0-6ubuntu1~16.04.11 [40.1 kB] build 30-May-2019 23:23:30 Get:94 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmpx0 amd64 5.4.0-6ubuntu1~16.04.11 [9748 B] build 30-May-2019 23:23:30 Get:95 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libquadmath0 amd64 5.4.0-6ubuntu1~16.04.11 [131 kB] build 30-May-2019 23:23:30 Get:96 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgcc-5-dev amd64 5.4.0-6ubuntu1~16.04.11 [2229 kB] build 30-May-2019 23:23:30 Get:97 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 gcc-5 amd64 5.4.0-6ubuntu1~16.04.11 [8417 kB] build 30-May-2019 23:23:31 Get:98 http://archive.ubuntu.com/ubuntu xenial/main amd64 gcc amd64 4:5.3.1-1ubuntu1 [5244 B] build 30-May-2019 23:23:31 Get:99 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libstdc++-5-dev amd64 5.4.0-6ubuntu1~16.04.11 [1426 kB] build 30-May-2019 23:23:31 Get:100 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 g++-5 amd64 5.4.0-6ubuntu1~16.04.11 [8310 kB] build 30-May-2019 23:23:31 Get:101 http://archive.ubuntu.com/ubuntu xenial/main amd64 g++ amd64 4:5.3.1-1ubuntu1 [1504 B] build 30-May-2019 23:23:31 Get:102 http://archive.ubuntu.com/ubuntu xenial/main amd64 make amd64 4.1-6 [151 kB] build 30-May-2019 23:23:31 Get:103 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libdpkg-perl all 1.18.4ubuntu1.5 [195 kB] build 30-May-2019 23:23:31 Get:104 http://archive.ubuntu.com/ubuntu xenial/main amd64 xz-utils amd64 5.1.1alpha+20120614-2ubuntu2 [78.8 kB] build 30-May-2019 23:23:32 Get:105 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 patch amd64 2.7.5-1ubuntu0.16.04.1 [90.5 kB] build 30-May-2019 23:23:32 Get:106 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 dpkg-dev all 1.18.4ubuntu1.5 [584 kB] build 30-May-2019 23:23:32 Get:107 http://archive.ubuntu.com/ubuntu xenial/main amd64 build-essential amd64 12.1ubuntu2 [4758 B] build 30-May-2019 23:23:32 Get:108 http://archive.ubuntu.com/ubuntu xenial/main amd64 libcroco3 amd64 0.6.11-1 [81.6 kB] build 30-May-2019 23:23:32 Get:109 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 gettext amd64 0.19.7-2ubuntu3.1 [1082 kB] build 30-May-2019 23:23:32 Get:110 http://archive.ubuntu.com/ubuntu xenial/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] build 30-May-2019 23:23:32 Get:111 http://archive.ubuntu.com/ubuntu xenial/main amd64 po-debconf all 1.0.19 [234 kB] build 30-May-2019 23:23:32 Get:112 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libarchive-zip-perl all 1.56-2ubuntu0.1 [84.7 kB] build 30-May-2019 23:23:32 Get:113 http://archive.ubuntu.com/ubuntu xenial/main amd64 libfile-stripnondeterminism-perl all 0.015-1 [10.3 kB] build 30-May-2019 23:23:32 Get:114 http://archive.ubuntu.com/ubuntu xenial/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] build 30-May-2019 23:23:32 Get:115 http://archive.ubuntu.com/ubuntu xenial/main amd64 dh-strip-nondeterminism all 0.015-1 [4864 B] build 30-May-2019 23:23:32 Get:116 http://archive.ubuntu.com/ubuntu xenial/main amd64 debhelper all 9.20160115ubuntu3 [739 kB] build 30-May-2019 23:23:32 Get:117 http://archive.ubuntu.com/ubuntu xenial/main amd64 liburi-perl all 1.71-1 [76.9 kB] build 30-May-2019 23:23:32 Get:118 http://archive.ubuntu.com/ubuntu xenial/main amd64 libencode-locale-perl all 1.05-1 [12.3 kB] build 30-May-2019 23:23:32 Get:119 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhttp-date-perl all 6.02-1 [10.4 kB] build 30-May-2019 23:23:32 Get:120 http://archive.ubuntu.com/ubuntu xenial/main amd64 libfile-listing-perl all 6.04-1 [9774 B] build 30-May-2019 23:23:32 Get:121 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhtml-tagset-perl all 3.20-2 [13.5 kB] build 30-May-2019 23:23:32 Get:122 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhtml-parser-perl amd64 3.72-1 [86.1 kB] build 30-May-2019 23:23:32 Get:123 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhtml-tree-perl all 5.03-2 [197 kB] build 30-May-2019 23:23:32 Get:124 http://archive.ubuntu.com/ubuntu xenial/main amd64 libio-html-perl all 1.001-1 [14.9 kB] build 30-May-2019 23:23:32 Get:125 http://archive.ubuntu.com/ubuntu xenial/main amd64 liblwp-mediatypes-perl all 6.02-1 [21.7 kB] build 30-May-2019 23:23:32 Get:126 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhttp-message-perl all 6.11-1 [74.3 kB] build 30-May-2019 23:23:32 Get:127 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhttp-cookies-perl all 6.01-1 [17.2 kB] build 30-May-2019 23:23:32 Get:128 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhttp-negotiate-perl all 6.00-2 [13.4 kB] build 30-May-2019 23:23:33 Get:129 http://archive.ubuntu.com/ubuntu xenial/main amd64 libnet-ssleay-perl amd64 1.72-1build1 [259 kB] build 30-May-2019 23:23:33 Get:130 http://archive.ubuntu.com/ubuntu xenial/main amd64 libio-socket-ssl-perl all 2.024-1 [159 kB] build 30-May-2019 23:23:33 Get:131 http://archive.ubuntu.com/ubuntu xenial/main amd64 libnet-http-perl all 6.09-1 [24.0 kB] build 30-May-2019 23:23:33 Get:132 http://archive.ubuntu.com/ubuntu xenial/main amd64 liblwp-protocol-https-perl all 6.06-2 [8682 B] build 30-May-2019 23:23:33 Get:133 http://archive.ubuntu.com/ubuntu xenial/main amd64 libwww-robotrules-perl all 6.01-1 [14.1 kB] build 30-May-2019 23:23:33 Get:134 http://archive.ubuntu.com/ubuntu xenial/main amd64 libwww-perl all 6.15-1 [146 kB] build 30-May-2019 23:23:33 Get:135 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxml-parser-perl amd64 2.44-1build1 [200 kB] build 30-May-2019 23:23:33 Get:136 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 intltool all 0.51.0-2ubuntu1.16.04.1 [45.0 kB] build 30-May-2019 23:23:33 Get:137 http://archive.ubuntu.com/ubuntu xenial/main amd64 dh-translations all 129 [22.1 kB] build 30-May-2019 23:23:33 Get:138 http://archive.ubuntu.com/ubuntu xenial/main amd64 python-six all 1.10.0-3 [10.9 kB] build 30-May-2019 23:23:33 Get:139 http://archive.ubuntu.com/ubuntu xenial/main amd64 python-pkg-resources all 20.7.0-1 [108 kB] build 30-May-2019 23:23:33 Get:140 http://archive.ubuntu.com/ubuntu xenial/main amd64 python-scour all 0.32-1 [42.7 kB] build 30-May-2019 23:23:33 Get:141 http://archive.ubuntu.com/ubuntu xenial/main amd64 cdbs all 0.4.130ubuntu2 [42.8 kB] build 30-May-2019 23:23:33 Get:142 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgfortran3 amd64 5.4.0-6ubuntu1~16.04.11 [260 kB] build 30-May-2019 23:23:33 Get:143 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgfortran-5-dev amd64 5.4.0-6ubuntu1~16.04.11 [291 kB] build 30-May-2019 23:23:33 Get:144 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 gfortran-5 amd64 5.4.0-6ubuntu1~16.04.11 [8034 kB] build 30-May-2019 23:23:33 Get:145 http://archive.ubuntu.com/ubuntu xenial/main amd64 gfortran amd64 4:5.3.1-1ubuntu1 [1288 B] build 30-May-2019 23:23:33 Get:146 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 icu-devtools amd64 55.1-7ubuntu0.4 [166 kB] build 30-May-2019 23:23:33 Get:147 http://archive.ubuntu.com/ubuntu xenial/main amd64 libblas-common amd64 3.6.0-2ubuntu2 [5342 B] build 30-May-2019 23:23:33 Get:148 http://archive.ubuntu.com/ubuntu xenial/main amd64 libblas3 amd64 3.6.0-2ubuntu2 [147 kB] build 30-May-2019 23:23:33 Get:149 http://archive.ubuntu.com/ubuntu xenial/main amd64 libblas-dev amd64 3.6.0-2ubuntu2 [153 kB] build 30-May-2019 23:23:33 Get:150 http://archive.ubuntu.com/ubuntu xenial/main amd64 libbz2-dev amd64 1.0.6-8 [29.1 kB] build 30-May-2019 23:23:33 Get:151 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpixman-1-0 amd64 0.33.6-1 [231 kB] build 30-May-2019 23:23:33 Get:152 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-render0 amd64 1.11.1-1ubuntu1 [11.4 kB] build 30-May-2019 23:23:33 Get:153 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-shm0 amd64 1.11.1-1ubuntu1 [5588 B] build 30-May-2019 23:23:33 Get:154 http://archive.ubuntu.com/ubuntu xenial/main amd64 libcairo2 amd64 1.14.6-1 [555 kB] build 30-May-2019 23:23:33 Get:155 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libcurl3 amd64 7.47.0-1ubuntu2.13 [186 kB] build 30-May-2019 23:23:33 Get:156 http://archive.ubuntu.com/ubuntu xenial/main amd64 libdatrie1 amd64 0.2.10-2 [17.3 kB] build 30-May-2019 23:23:33 Get:157 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgraphite2-3 amd64 1.3.10-0ubuntu0.16.04.1 [71.7 kB] build 30-May-2019 23:23:33 Get:158 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libharfbuzz0b amd64 1.0.1-1ubuntu0.1 [140 kB] build 30-May-2019 23:23:33 Get:159 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libicu-dev amd64 55.1-7ubuntu0.4 [8566 kB] build 30-May-2019 23:23:33 Get:160 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libjpeg-turbo8-dev amd64 1.4.2-0ubuntu3.1 [254 kB] build 30-May-2019 23:23:33 Get:161 http://archive.ubuntu.com/ubuntu xenial/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] build 30-May-2019 23:23:33 Get:162 http://archive.ubuntu.com/ubuntu xenial/main amd64 libjpeg8-dev amd64 8c-2ubuntu8 [1552 B] build 30-May-2019 23:23:33 Get:163 http://archive.ubuntu.com/ubuntu xenial/main amd64 libjpeg-dev amd64 8c-2ubuntu8 [1546 B] build 30-May-2019 23:23:33 Get:164 http://archive.ubuntu.com/ubuntu xenial/main amd64 liblapack3 amd64 3.6.0-2ubuntu2 [1938 kB] build 30-May-2019 23:23:33 Get:165 http://archive.ubuntu.com/ubuntu xenial/main amd64 liblapack-dev amd64 3.6.0-2ubuntu2 [1948 kB] build 30-May-2019 23:23:34 Get:166 http://archive.ubuntu.com/ubuntu xenial/main amd64 libtinfo-dev amd64 6.0+20160213-1ubuntu1 [77.4 kB] build 30-May-2019 23:23:34 Get:167 http://archive.ubuntu.com/ubuntu xenial/main amd64 libncurses5-dev amd64 6.0+20160213-1ubuntu1 [175 kB] build 30-May-2019 23:23:34 Get:168 http://archive.ubuntu.com/ubuntu xenial/main amd64 libthai-data all 0.1.24-2 [131 kB] build 30-May-2019 23:23:34 Get:169 http://archive.ubuntu.com/ubuntu xenial/main amd64 libthai0 amd64 0.1.24-2 [17.3 kB] build 30-May-2019 23:23:34 Get:170 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpango-1.0-0 amd64 1.38.1-1 [148 kB] build 30-May-2019 23:23:34 Get:171 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpangoft2-1.0-0 amd64 1.38.1-1 [33.3 kB] build 30-May-2019 23:23:34 Get:172 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpangocairo-1.0-0 amd64 1.38.1-1 [20.5 kB] build 30-May-2019 23:23:34 Get:173 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpaper1 amd64 1.1.24+nmu4ubuntu1 [13.7 kB] build 30-May-2019 23:23:34 Get:174 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpaper-utils amd64 1.1.24+nmu4ubuntu1 [8276 B] build 30-May-2019 23:23:34 Get:175 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpcre16-3 amd64 2:8.38-3.1 [144 kB] build 30-May-2019 23:23:34 Get:176 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpcre32-3 amd64 2:8.38-3.1 [136 kB] build 30-May-2019 23:23:34 Get:177 http://archive.ubuntu.com/ubuntu xenial/main amd64 libpcre3-dev amd64 2:8.38-3.1 [525 kB] build 30-May-2019 23:23:34 Get:178 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2ubuntu4.1 [168 kB] build 30-May-2019 23:23:34 Get:179 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpng12-dev amd64 1.2.54-1ubuntu1.1 [183 kB] build 30-May-2019 23:23:34 Get:180 http://archive.ubuntu.com/ubuntu xenial/main amd64 libreadline6-dev amd64 6.3-8ubuntu2 [124 kB] build 30-May-2019 23:23:34 Get:181 http://archive.ubuntu.com/ubuntu xenial/main amd64 libreadline-dev amd64 6.3-8ubuntu2 [992 B] build 30-May-2019 23:23:34 Get:182 http://archive.ubuntu.com/ubuntu xenial/main amd64 libtcl8.6 amd64 8.6.5+dfsg-2 [875 kB] build 30-May-2019 23:23:34 Get:183 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtiff5 amd64 4.0.6-1ubuntu0.6 [149 kB] build 30-May-2019 23:23:34 Get:184 http://archive.ubuntu.com/ubuntu xenial/main amd64 libtk8.6 amd64 8.6.5-1 [693 kB] build 30-May-2019 23:23:34 Get:185 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxt6 amd64 1:1.1.5-0ubuntu1 [160 kB] build 30-May-2019 23:23:34 Get:186 http://archive.ubuntu.com/ubuntu xenial/main amd64 pkg-config amd64 0.29.1-0ubuntu1 [45.0 kB] build 30-May-2019 23:23:34 Get:187 http://archive.ubuntu.com/ubuntu xenial/main amd64 zip amd64 3.0-11 [158 kB] build 30-May-2019 23:23:34 Get:188 http://archive.ubuntu.com/ubuntu xenial/main amd64 unzip amd64 6.0-20ubuntu1 [158 kB] build 30-May-2019 23:23:34 Get:189 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 xdg-utils all 1.1.1-1ubuntu1.16.04.3 [59.6 kB] build 30-May-2019 23:23:34 Get:190 http://archive.ubuntu.com/ubuntu xenial/main amd64 liblzma-dev amd64 5.1.1alpha+20120614-2ubuntu2 [137 kB] build 30-May-2019 23:23:34 debconf: delaying package configuration, since apt-utils is not installed build 30-May-2019 23:23:34 Fetched 116 MB in 7s (16.3 MB/s) build 30-May-2019 23:23:35 Selecting previously unselected package libgdbm3:amd64. build 30-May-2019 23:23:35 (Reading database ... build 30-May-2019 23:23:35 (Reading database ... 5% build 30-May-2019 23:23:35 (Reading database ... 10% build 30-May-2019 23:23:35 (Reading database ... 15% build 30-May-2019 23:23:35 (Reading database ... 20% build 30-May-2019 23:23:35 (Reading database ... 25% build 30-May-2019 23:23:35 (Reading database ... 30% build 30-May-2019 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build 30-May-2019 23:25:29 Selecting previously unselected package r-base-dev. build 30-May-2019 23:25:29 Preparing to unpack .../r-base-dev_3.4.4-1xenial0_all.deb ... build 30-May-2019 23:25:29 Unpacking r-base-dev (3.4.4-1xenial0) ... build 30-May-2019 23:25:29 Processing triggers for libc-bin (2.23-0ubuntu11) ... build 30-May-2019 23:25:29 Processing triggers for mime-support (3.59ubuntu1) ... build 30-May-2019 23:25:29 Processing triggers for systemd (229-4ubuntu21.21) ... build 30-May-2019 23:25:30 Setting up libgdbm3:amd64 (1.8.3-13.1) ... build 30-May-2019 23:25:30 Setting up libglib2.0-0:amd64 (2.48.2-0ubuntu4.1) ... build 30-May-2019 23:25:30 No schema files found: doing nothing. build 30-May-2019 23:25:30 Setting up libxau6:amd64 (1:1.0.8-1) ... build 30-May-2019 23:25:30 Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ... build 30-May-2019 23:25:30 Setting up libxcb1:amd64 (1.11.1-1ubuntu1) ... build 30-May-2019 23:25:31 Setting up libx11-data (2:1.6.3-1ubuntu2.1) ... build 30-May-2019 23:25:31 Setting up libx11-6:amd64 (2:1.6.3-1ubuntu2.1) ... build 30-May-2019 23:25:31 Setting up libxext6:amd64 (2:1.3.3-1) ... build 30-May-2019 23:25:32 Setting up groff-base (1.22.3-7) ... build 30-May-2019 23:25:32 Setting up bsdmainutils (9.0.6ubuntu3) ... build 30-May-2019 23:25:33 update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode build 30-May-2019 23:25:33 update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode build 30-May-2019 23:25:33 Setting up libpipeline1:amd64 (1.4.1-2) ... build 30-May-2019 23:25:33 Setting up man-db (2.7.5-1) ... build 30-May-2019 23:25:33 debconf: unable to initialize frontend: Dialog build 30-May-2019 23:25:33 debconf: (TERM is not set, so the dialog frontend is not usable.) build 30-May-2019 23:25:33 debconf: falling back to frontend: Readline build 30-May-2019 23:25:33 Building database of manual pages ... build 30-May-2019 23:25:43 Setting up fonts-dejavu-core (2.35-1) ... build 30-May-2019 23:25:44 Setting up ucf (3.0036) ... build 30-May-2019 23:25:44 debconf: unable to initialize frontend: Dialog build 30-May-2019 23:25:44 debconf: (TERM is not set, so the dialog frontend is not usable.) build 30-May-2019 23:25:44 debconf: falling back to frontend: Readline build 30-May-2019 23:25:44 Setting up fontconfig-config (2.11.94-0ubuntu1.1) ... build 30-May-2019 23:25:46 Setting up libpng12-0:amd64 (1.2.54-1ubuntu1.1) ... build 30-May-2019 23:25:46 Setting up libfreetype6:amd64 (2.6.1-0.1ubuntu2.3) ... build 30-May-2019 23:25:47 Setting up libfontconfig1:amd64 (2.11.94-0ubuntu1.1) ... build 30-May-2019 23:25:47 Setting up fontconfig (2.11.94-0ubuntu1.1) ... build 30-May-2019 23:25:50 Regenerating fonts cache... done. build 30-May-2019 23:25:50 Setting up x11-common (1:7.7+13ubuntu3.1) ... build 30-May-2019 23:25:51 debconf: unable to initialize frontend: Dialog build 30-May-2019 23:25:51 debconf: (TERM is not set, so the dialog frontend is not usable.) build 30-May-2019 23:25:51 debconf: falling back to frontend: Readline build 30-May-2019 23:25:51 update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults build 30-May-2019 23:25:51 invoke-rc.d: could not determine current runlevel build 30-May-2019 23:25:51 invoke-rc.d: policy-rc.d denied execution of start. build 30-May-2019 23:25:51 Setting up libice6:amd64 (2:1.0.9-1) ... build 30-May-2019 23:25:51 Setting up libjpeg-turbo8:amd64 (1.4.2-0ubuntu3.1) ... build 30-May-2019 23:25:51 Setting up libpcrecpp0v5:amd64 (2:8.38-3.1) ... build 30-May-2019 23:25:51 Setting up libsigsegv2:amd64 (2.10-4) ... build 30-May-2019 23:25:51 Setting up libsm6:amd64 (2:1.2.2-1) ... build 30-May-2019 23:25:52 Setting up libunistring0:amd64 (0.9.3-5.2ubuntu1) ... build 30-May-2019 23:25:52 Setting up libxrender1:amd64 (1:0.9.9-0ubuntu1) ... build 30-May-2019 23:25:52 Setting up libxft2:amd64 (2.3.2-1) ... build 30-May-2019 23:25:53 Setting up libxss1:amd64 (1:1.2.2-1) ... build 30-May-2019 23:25:53 Setting up perl-modules-5.22 (5.22.1-9ubuntu0.6) ... build 30-May-2019 23:25:54 Setting up libperl5.22:amd64 (5.22.1-9ubuntu0.6) ... build 30-May-2019 23:25:54 Setting up perl (5.22.1-9ubuntu0.6) ... build 30-May-2019 23:25:54 update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode build 30-May-2019 23:25:54 Setting up libjbig0:amd64 (2.1-3.1) ... build 30-May-2019 23:25:54 Setting up libgmp10:amd64 (2:6.1.0+dfsg-2) ... build 30-May-2019 23:25:54 Setting up libmpfr4:amd64 (3.1.4-1) ... build 30-May-2019 23:25:55 Setting up libmpc3:amd64 (1.0.3-1) ... build 30-May-2019 23:25:55 Setting up tzdata (2019a-0ubuntu0.16.04) ... build 30-May-2019 23:25:55 debconf: unable to initialize frontend: Dialog build 30-May-2019 23:25:55 debconf: (TERM is not set, so the dialog frontend is not usable.) build 30-May-2019 23:25:55 debconf: falling back to frontend: Readline build 30-May-2019 23:25:55 build 30-May-2019 23:25:55 Current default time zone: 'Etc/UTC' build 30-May-2019 23:25:55 Local time is now: Fri May 31 04:25:55 UTC 2019. build 30-May-2019 23:25:55 Universal Time is now: Fri May 31 04:25:55 UTC 2019. build 30-May-2019 23:25:55 Run 'dpkg-reconfigure tzdata' if you wish to change it. build 30-May-2019 23:25:55 build 30-May-2019 23:25:55 Setting up bzip2 (1.0.6-8) ... build 30-May-2019 23:25:55 Setting up libmagic1:amd64 (1:5.25-2ubuntu1.2) ... build 30-May-2019 23:25:56 Setting up file (1:5.25-2ubuntu1.2) ... build 30-May-2019 23:25:56 Setting up libnettle6:amd64 (3.2-1ubuntu0.16.04.1) ... build 30-May-2019 23:25:56 Setting up libhogweed4:amd64 (3.2-1ubuntu0.16.04.1) ... build 30-May-2019 23:25:56 Setting up libidn11:amd64 (1.32-3ubuntu1.2) ... build 30-May-2019 23:25:56 Setting up libp11-kit0:amd64 (0.23.2-5~ubuntu16.04.1) ... build 30-May-2019 23:25:56 Setting up libtasn1-6:amd64 (4.7-3ubuntu0.16.04.3) ... build 30-May-2019 23:25:57 Setting up libgnutls30:amd64 (3.4.10-4ubuntu1.5) ... build 30-May-2019 23:25:57 Setting up netbase (5.3) ... build 30-May-2019 23:25:58 Setting up libasprintf0v5:amd64 (0.19.7-2ubuntu3.1) ... build 30-May-2019 23:25:58 Setting up gettext-base (0.19.7-2ubuntu3.1) ... build 30-May-2019 23:25:59 Setting up libroken18-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ... build 30-May-2019 23:25:59 Setting up libasn1-8-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ... build 30-May-2019 23:25:59 Setting up libkrb5support0:amd64 (1.13.2+dfsg-5ubuntu2.1) ... build 30-May-2019 23:25:59 Setting up libk5crypto3:amd64 (1.13.2+dfsg-5ubuntu2.1) ... build 30-May-2019 23:25:59 Setting up libkeyutils1:amd64 (1.5.9-8ubuntu1) ... build 30-May-2019 23:25:59 Setting up libkrb5-3:amd64 (1.13.2+dfsg-5ubuntu2.1) ... build 30-May-2019 23:25:59 Setting up libgssapi-krb5-2:amd64 (1.13.2+dfsg-5ubuntu2.1) ... build 30-May-2019 23:26:00 Setting up libhcrypto4-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ... build 30-May-2019 23:26:00 Setting up libheimbase1-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ... build 30-May-2019 23:26:00 Setting up libwind0-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ... build 30-May-2019 23:26:00 Setting up libhx509-5-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ... build 30-May-2019 23:26:00 Setting up libkrb5-26-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ... build 30-May-2019 23:26:00 Setting up libheimntlm0-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ... build 30-May-2019 23:26:01 Setting up libgssapi3-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ... build 30-May-2019 23:26:01 Setting up libicu55:amd64 (55.1-7ubuntu0.4) ... build 30-May-2019 23:26:01 Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-14ubuntu0.1) ... build 30-May-2019 23:26:01 Setting up libsasl2-2:amd64 (2.1.26.dfsg1-14ubuntu0.1) ... build 30-May-2019 23:26:01 Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2ubuntu3.5) ... build 30-May-2019 23:26:01 Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d-1ubuntu0.1) ... build 30-May-2019 23:26:02 Setting up libxml2:amd64 (2.9.3+dfsg1-1ubuntu0.6) ... build 30-May-2019 23:26:02 Setting up libxmuu1:amd64 (2:1.1.2-2) ... build 30-May-2019 23:26:02 Setting up xauth (1:1.0.9-1ubuntu2) ... build 30-May-2019 23:26:02 Setting up m4 (1.4.17-5) ... build 30-May-2019 23:26:02 Setting up autoconf (2.69-9) ... build 30-May-2019 23:26:02 Setting up autotools-dev (20150820.1) ... build 30-May-2019 23:26:02 Setting up automake (1:1.15-4ubuntu1) ... build 30-May-2019 23:26:03 update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode build 30-May-2019 23:26:03 Setting up binutils (2.26.1-1ubuntu1~16.04.8) ... build 30-May-2019 23:26:03 Setting up libc-dev-bin (2.23-0ubuntu11) ... build 30-May-2019 23:26:03 Setting up linux-libc-dev:amd64 (4.4.0-148.174) ... build 30-May-2019 23:26:03 Setting up libc6-dev:amd64 (2.23-0ubuntu11) ... build 30-May-2019 23:26:04 Setting up libisl15:amd64 (0.16.1-1) ... build 30-May-2019 23:26:04 Setting up cpp-5 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:05 Setting up cpp (4:5.3.1-1ubuntu1) ... build 30-May-2019 23:26:05 Setting up libcc1-0:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:05 Setting up libgomp1:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:05 Setting up libitm1:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:05 Setting up libatomic1:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:06 Setting up libasan2:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:06 Setting up liblsan0:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:06 Setting up libtsan0:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:06 Setting up libubsan0:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:06 Setting up libcilkrts5:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:06 Setting up libmpx0:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:07 Setting up libquadmath0:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:07 Setting up libgcc-5-dev:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:07 Setting up gcc-5 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:08 Setting up gcc (4:5.3.1-1ubuntu1) ... build 30-May-2019 23:26:08 Setting up libstdc++-5-dev:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:08 Setting up g++-5 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:09 Setting up g++ (4:5.3.1-1ubuntu1) ... build 30-May-2019 23:26:09 update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode build 30-May-2019 23:26:09 Setting up make (4.1-6) ... build 30-May-2019 23:26:09 Setting up libdpkg-perl (1.18.4ubuntu1.5) ... build 30-May-2019 23:26:09 Setting up xz-utils (5.1.1alpha+20120614-2ubuntu2) ... build 30-May-2019 23:26:09 update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode build 30-May-2019 23:26:09 Setting up patch (2.7.5-1ubuntu0.16.04.1) ... build 30-May-2019 23:26:09 Setting up dpkg-dev (1.18.4ubuntu1.5) ... build 30-May-2019 23:26:10 Setting up build-essential (12.1ubuntu2) ... build 30-May-2019 23:26:10 Setting up libcroco3:amd64 (0.6.11-1) ... build 30-May-2019 23:26:10 Setting up gettext (0.19.7-2ubuntu3.1) ... build 30-May-2019 23:26:11 Setting up intltool-debian (0.35.0+20060710.4) ... build 30-May-2019 23:26:11 Setting up po-debconf (1.0.19) ... build 30-May-2019 23:26:11 Setting up libarchive-zip-perl (1.56-2ubuntu0.1) ... build 30-May-2019 23:26:12 Setting up libfile-stripnondeterminism-perl (0.015-1) ... build 30-May-2019 23:26:12 Setting up libtimedate-perl (2.3000-2) ... build 30-May-2019 23:26:12 Setting up liburi-perl (1.71-1) ... build 30-May-2019 23:26:12 Setting up libencode-locale-perl (1.05-1) ... build 30-May-2019 23:26:12 Setting up libhttp-date-perl (6.02-1) ... build 30-May-2019 23:26:12 Setting up libfile-listing-perl (6.04-1) ... build 30-May-2019 23:26:13 Setting up libhtml-tagset-perl (3.20-2) ... build 30-May-2019 23:26:13 Setting up libhtml-parser-perl (3.72-1) ... build 30-May-2019 23:26:13 Setting up libhtml-tree-perl (5.03-2) ... build 30-May-2019 23:26:13 Setting up libio-html-perl (1.001-1) ... build 30-May-2019 23:26:13 Setting up liblwp-mediatypes-perl (6.02-1) ... build 30-May-2019 23:26:13 Setting up libhttp-message-perl (6.11-1) ... build 30-May-2019 23:26:13 Setting up libhttp-cookies-perl (6.01-1) ... build 30-May-2019 23:26:14 Setting up libhttp-negotiate-perl (6.00-2) ... build 30-May-2019 23:26:14 Setting up libnet-ssleay-perl (1.72-1build1) ... build 30-May-2019 23:26:14 Setting up libio-socket-ssl-perl (2.024-1) ... build 30-May-2019 23:26:14 Setting up libnet-http-perl (6.09-1) ... build 30-May-2019 23:26:14 Setting up libwww-robotrules-perl (6.01-1) ... build 30-May-2019 23:26:14 Setting up python-six (1.10.0-3) ... build 30-May-2019 23:26:15 Setting up python-pkg-resources (20.7.0-1) ... build 30-May-2019 23:26:17 Setting up python-scour (0.32-1) ... build 30-May-2019 23:26:18 Setting up libgfortran3:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:18 Setting up libgfortran-5-dev:amd64 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:18 Setting up gfortran-5 (5.4.0-6ubuntu1~16.04.11) ... build 30-May-2019 23:26:18 Setting up gfortran (4:5.3.1-1ubuntu1) ... build 30-May-2019 23:26:18 update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode build 30-May-2019 23:26:19 update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode build 30-May-2019 23:26:19 Setting up icu-devtools (55.1-7ubuntu0.4) ... build 30-May-2019 23:26:19 Setting up libblas-common (3.6.0-2ubuntu2) ... build 30-May-2019 23:26:19 Setting up libblas3 (3.6.0-2ubuntu2) ... build 30-May-2019 23:26:19 update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode build 30-May-2019 23:26:19 Setting up libblas-dev (3.6.0-2ubuntu2) ... build 30-May-2019 23:26:19 update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode build 30-May-2019 23:26:19 Setting up libbz2-dev:amd64 (1.0.6-8) ... build 30-May-2019 23:26:19 Setting up libpixman-1-0:amd64 (0.33.6-1) ... build 30-May-2019 23:26:20 Setting up libxcb-render0:amd64 (1.11.1-1ubuntu1) ... build 30-May-2019 23:26:20 Setting up libxcb-shm0:amd64 (1.11.1-1ubuntu1) ... build 30-May-2019 23:26:20 Setting up libcairo2:amd64 (1.14.6-1) ... build 30-May-2019 23:26:20 Setting up libcurl3:amd64 (7.47.0-1ubuntu2.13) ... build 30-May-2019 23:26:20 Setting up libdatrie1:amd64 (0.2.10-2) ... build 30-May-2019 23:26:20 Setting up libgraphite2-3:amd64 (1.3.10-0ubuntu0.16.04.1) ... build 30-May-2019 23:26:21 Setting up libharfbuzz0b:amd64 (1.0.1-1ubuntu0.1) ... build 30-May-2019 23:26:21 Setting up libicu-dev:amd64 (55.1-7ubuntu0.4) ... build 30-May-2019 23:26:21 Setting up libjpeg-turbo8-dev:amd64 (1.4.2-0ubuntu3.1) ... build 30-May-2019 23:26:22 Setting up libjpeg8:amd64 (8c-2ubuntu8) ... build 30-May-2019 23:26:22 Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ... build 30-May-2019 23:26:22 Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... build 30-May-2019 23:26:23 Setting up liblapack3 (3.6.0-2ubuntu2) ... build 30-May-2019 23:26:23 update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode build 30-May-2019 23:26:23 Setting up liblapack-dev (3.6.0-2ubuntu2) ... build 30-May-2019 23:26:23 update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode build 30-May-2019 23:26:23 Setting up libtinfo-dev:amd64 (6.0+20160213-1ubuntu1) ... build 30-May-2019 23:26:23 Setting up libncurses5-dev:amd64 (6.0+20160213-1ubuntu1) ... build 30-May-2019 23:26:23 Setting up libthai-data (0.1.24-2) ... build 30-May-2019 23:26:24 Setting up libthai0:amd64 (0.1.24-2) ... build 30-May-2019 23:26:24 Setting up libpango-1.0-0:amd64 (1.38.1-1) ... build 30-May-2019 23:26:24 Setting up libpangoft2-1.0-0:amd64 (1.38.1-1) ... build 30-May-2019 23:26:24 Setting up libpangocairo-1.0-0:amd64 (1.38.1-1) ... build 30-May-2019 23:26:24 Setting up libpaper1:amd64 (1.1.24+nmu4ubuntu1) ... build 30-May-2019 23:26:24 debconf: unable to initialize frontend: Dialog build 30-May-2019 23:26:24 debconf: (TERM is not set, so the dialog frontend is not usable.) build 30-May-2019 23:26:24 debconf: falling back to frontend: Readline build 30-May-2019 23:26:24 build 30-May-2019 23:26:24 Creating config file /etc/papersize with new version build 30-May-2019 23:26:25 Setting up libpaper-utils (1.1.24+nmu4ubuntu1) ... build 30-May-2019 23:26:25 Setting up libpcre16-3:amd64 (2:8.38-3.1) ... build 30-May-2019 23:26:25 Setting up libpcre32-3:amd64 (2:8.38-3.1) ... build 30-May-2019 23:26:26 Setting up libpcre3-dev:amd64 (2:8.38-3.1) ... build 30-May-2019 23:26:26 Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2ubuntu4.1) ... build 30-May-2019 23:26:26 Setting up libpng12-dev:amd64 (1.2.54-1ubuntu1.1) ... build 30-May-2019 23:26:26 Setting up libreadline6-dev:amd64 (6.3-8ubuntu2) ... build 30-May-2019 23:26:27 Setting up libreadline-dev:amd64 (6.3-8ubuntu2) ... build 30-May-2019 23:26:27 Setting up libtcl8.6:amd64 (8.6.5+dfsg-2) ... build 30-May-2019 23:26:27 Setting up libtiff5:amd64 (4.0.6-1ubuntu0.6) ... build 30-May-2019 23:26:27 Setting up libtk8.6:amd64 (8.6.5-1) ... build 30-May-2019 23:26:27 Setting up libxt6:amd64 (1:1.1.5-0ubuntu1) ... build 30-May-2019 23:26:27 Setting up pkg-config (0.29.1-0ubuntu1) ... build 30-May-2019 23:26:28 Setting up zip (3.0-11) ... build 30-May-2019 23:26:28 Setting up unzip (6.0-20ubuntu1) ... build 30-May-2019 23:26:28 Setting up xdg-utils (1.1.1-1ubuntu1.16.04.3) ... build 30-May-2019 23:26:28 Setting up r-base-core (3.4.4-1xenial0) ... build 30-May-2019 23:26:28 debconf: unable to initialize frontend: Dialog build 30-May-2019 23:26:28 debconf: (TERM is not set, so the dialog frontend is not usable.) build 30-May-2019 23:26:28 debconf: falling back to frontend: Readline build 30-May-2019 23:26:29 build 30-May-2019 23:26:29 Creating config file /etc/R/Renviron with new version build 30-May-2019 23:26:29 Setting up liblzma-dev:amd64 (5.1.1alpha+20120614-2ubuntu2) ... build 30-May-2019 23:26:29 Setting up debhelper (9.20160115ubuntu3) ... build 30-May-2019 23:26:29 Setting up libwww-perl (6.15-1) ... build 30-May-2019 23:26:29 Setting up libxml-parser-perl (2.44-1build1) ... build 30-May-2019 23:26:29 Setting up intltool (0.51.0-2ubuntu1.16.04.1) ... build 30-May-2019 23:26:29 Setting up dh-translations (129) ... build 30-May-2019 23:26:30 Setting up cdbs (0.4.130ubuntu2) ... build 30-May-2019 23:26:30 Setting up r-base-dev (3.4.4-1xenial0) ... build 30-May-2019 23:26:30 Setting up dh-strip-nondeterminism (0.015-1) ... build 30-May-2019 23:26:31 Setting up liblwp-protocol-https-perl (6.06-2) ... build 30-May-2019 23:26:31 Processing triggers for libc-bin (2.23-0ubuntu11) ... build 30-May-2019 23:26:31 Processing triggers for systemd (229-4ubuntu21.21) ... build 30-May-2019 23:26:32 Installing package into '/usr/local/lib/R/site-library' build 30-May-2019 23:26:32 (as 'lib' is unspecified) build 30-May-2019 23:26:32 trying URL 'http://cran.rstudio.com/src/contrib/jsonlite_1.6.tar.gz' build 30-May-2019 23:26:33 Content type 'application/x-gzip' length 1052728 bytes (1.0 MB) build 30-May-2019 23:26:33 ================================================== build 30-May-2019 23:26:33 downloaded 1.0 MB build 30-May-2019 23:26:33 build 30-May-2019 23:26:33 * installing *source* package 'jsonlite' ... build 30-May-2019 23:26:33 ** package 'jsonlite' successfully unpacked and MD5 sums checked build 30-May-2019 23:26:33 ** libs build 30-May-2019 23:26:33 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o build 30-May-2019 23:26:33 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c collapse_array.c -o collapse_array.o build 30-May-2019 23:26:33 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c collapse_object.c -o collapse_object.o build 30-May-2019 23:26:33 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c collapse_pretty.c -o collapse_pretty.o build 30-May-2019 23:26:33 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c escape_chars.c -o escape_chars.o build 30-May-2019 23:26:33 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integer64_to_na.c -o integer64_to_na.o build 30-May-2019 23:26:33 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_datelist.c -o is_datelist.o build 30-May-2019 23:26:33 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_recordlist.c -o is_recordlist.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_scalarlist.c -o is_scalarlist.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c modp_numtoa.c -o modp_numtoa.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c null_to_na.c -o null_to_na.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c num_to_char.c -o num_to_char.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parse.c -o parse.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c prettify.c -o prettify.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c push_parser.c -o push_parser.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r-base64.c -o r-base64.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c register.c -o register.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c row_collapse.c -o row_collapse.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transpose_list.c -o transpose_list.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c validate.c -o validate.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl.c -o yajl/yajl.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o build 30-May-2019 23:26:34 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_buf.c -o yajl/yajl_buf.o build 30-May-2019 23:26:35 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_encode.c -o yajl/yajl_encode.o build 30-May-2019 23:26:35 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_gen.c -o yajl/yajl_gen.o build 30-May-2019 23:26:35 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_lex.c -o yajl/yajl_lex.o build 30-May-2019 23:26:35 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_parser.c -o yajl/yajl_parser.o build 30-May-2019 23:26:35 gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_tree.c -o yajl/yajl_tree.o build 30-May-2019 23:26:35 ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o build 30-May-2019 23:26:35 g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/usr/lib/R/lib -lR build 30-May-2019 23:26:35 installing to /usr/local/lib/R/site-library/jsonlite/libs build 30-May-2019 23:26:35 ** R build 30-May-2019 23:26:35 ** inst build 30-May-2019 23:26:35 ** preparing package for lazy loading build 30-May-2019 23:26:36 ** help build 30-May-2019 23:26:36 *** installing help indices build 30-May-2019 23:26:36 ** building package indices build 30-May-2019 23:26:36 ** installing vignettes build 30-May-2019 23:26:36 ** testing if installed package can be loaded build 30-May-2019 23:26:36 * DONE (jsonlite) build 30-May-2019 23:26:36  build 30-May-2019 23:26:36 The downloaded source packages are in build 30-May-2019 23:26:36 '/tmp/RtmpQLsVrQ/downloaded_packages' build 30-May-2019 23:26:36 [1] "/usr/local/lib/R/site-library/jsonlite" build 30-May-2019 23:26:43 Removing intermediate container 6e66337cf6c5 build 30-May-2019 23:26:43 ---> 2d3760fa8fb4 build 30-May-2019 23:26:43 Step 4/10 : COPY r_extractor.py launcher.R /home/clowder/ build 30-May-2019 23:26:44 ---> 6989934b3b5d build 30-May-2019 23:26:44 Step 5/10 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:26:44 ---> Running in aaa088559ad7 build 30-May-2019 23:26:45 Removing intermediate container aaa088559ad7 build 30-May-2019 23:26:45 ---> d0e5a7a64f6f build 30-May-2019 23:26:45 Step 6/10 : 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 30-May-2019 23:26:45 ---> Running in 854e9defdd59 build 30-May-2019 23:26:45 Removing intermediate container 854e9defdd59 build 30-May-2019 23:26:45 ---> 005a099d3f4a build 30-May-2019 23:26:45 Step 7/10 : ONBUILD COPY docker.R* Dockerfile /home/clowder/ build 30-May-2019 23:26:45 ---> Running in e4a0a90e398e build 30-May-2019 23:26:46 Removing intermediate container e4a0a90e398e build 30-May-2019 23:26:46 ---> 7cc834a1f567 build 30-May-2019 23:26:46 Step 8/10 : ONBUILD RUN if [ -e docker.R ]; then Rscript docker.R; fi build 30-May-2019 23:26:46 ---> Running in 18ad76844f9c build 30-May-2019 23:26:46 Removing intermediate container 18ad76844f9c build 30-May-2019 23:26:46 ---> 634c6259d143 build 30-May-2019 23:26:46 Step 9/10 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:26:46 ---> Running in 568f72279b9a build 30-May-2019 23:26:47 Removing intermediate container 568f72279b9a build 30-May-2019 23:26:47 ---> a3d77f40c658 build 30-May-2019 23:26:47 Step 10/10 : CMD python r_extractor.py build 30-May-2019 23:26:47 ---> Running in ff7e09422b5c build 30-May-2019 23:26:47 Removing intermediate container ff7e09422b5c build 30-May-2019 23:26:47 ---> 4a56839e2505 build 30-May-2019 23:26:47 Successfully built 4a56839e2505 build 30-May-2019 23:26:47 Successfully tagged clowder/extractors-simple-r-extractor:onbuild build 30-May-2019 23:26:47 Sending build context to Docker daemon 281.1kB build 30-May-2019 23:26:47 build 30-May-2019 23:26:47 Step 1/9 : FROM ubuntu:16.04 build 30-May-2019 23:26:47 ---> 2a697363a870 build 30-May-2019 23:26:47 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 30-May-2019 23:26:47 ---> Using cache build 30-May-2019 23:26:47 ---> 07339c96c1a7 build 30-May-2019 23:26:47 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 30-May-2019 23:26:47 ---> Using cache build 30-May-2019 23:26:47 ---> 66b8b13e8095 build 30-May-2019 23:26:47 Step 4/9 : COPY pyclowder /tmp/pyclowder/pyclowder build 30-May-2019 23:26:47 ---> Using cache build 30-May-2019 23:26:47 ---> d8c1b0c331b0 build 30-May-2019 23:26:47 Step 5/9 : COPY setup.py description.rst /tmp/pyclowder/ build 30-May-2019 23:26:47 ---> Using cache build 30-May-2019 23:26:47 ---> 53f00a224aaa build 30-May-2019 23:26:47 Step 6/9 : RUN pip install --upgrade /tmp/pyclowder && rm -rf /tmp/pyclowder build 30-May-2019 23:26:47 ---> Using cache build 30-May-2019 23:26:47 ---> eee101981043 build 30-May-2019 23:26:47 Step 7/9 : WORKDIR /home/clowder build 30-May-2019 23:26:47 ---> Using cache build 30-May-2019 23:26:47 ---> c91f4b8f86bc build 30-May-2019 23:26:47 Step 8/9 : COPY notifications.json /home/clowder build 30-May-2019 23:26:47 ---> Using cache build 30-May-2019 23:26:47 ---> dbc4c8fabc3a build 30-May-2019 23:26:47 Step 9/9 : CMD python "./${MAIN_SCRIPT}" build 30-May-2019 23:26:47 ---> Using cache build 30-May-2019 23:26:47 ---> e3941ef228e0 build 30-May-2019 23:26:47 [Warning] One or more build-args [PYTHON_VERSION] were not consumed build 30-May-2019 23:26:47 Successfully built e3941ef228e0 build 30-May-2019 23:26:47 Successfully tagged clowder/pyclowder-python3:latest build 30-May-2019 23:26:48 Sending build context to Docker daemon 279.6kB build 30-May-2019 23:26:48 build 30-May-2019 23:26:48 Step 1/6 : FROM clowder/pyclowder build 30-May-2019 23:26:48 ---> e3941ef228e0 build 30-May-2019 23:26:48 Step 2/6 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> b373d4266138 build 30-May-2019 23:26:48 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 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 8fd45ef39137 build 30-May-2019 23:26:48 Step 4/6 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> c483dc4e92f2 build 30-May-2019 23:26:48 Step 5/6 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> d19ae6315361 build 30-May-2019 23:26:48 Step 6/6 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 826af52f4fb4 build 30-May-2019 23:26:48 [Warning] One or more build-args [PYTHON_VERSION] were not consumed build 30-May-2019 23:26:48 Successfully built 826af52f4fb4 build 30-May-2019 23:26:48 Successfully tagged clowder/pyclowder-python3:onbuild build 30-May-2019 23:26:48 Sending build context to Docker daemon 6.656kB build 30-May-2019 23:26:48 build 30-May-2019 23:26:48 Step 1/9 : FROM clowder/pyclowder:onbuild build 30-May-2019 23:26:48 # Executing 5 build triggers build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 86ff6d69b221 build 30-May-2019 23:26:48 Step 2/9 : ENV EXTRACTION_FUNC="" build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> af366a91ccdd build 30-May-2019 23:26:48 Step 3/9 : ENV EXTRACTION_MODULE="" build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 5ccb678d30c6 build 30-May-2019 23:26:48 Step 4/9 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 5508388d0713 build 30-May-2019 23:26:48 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 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> a015d01ce7f7 build 30-May-2019 23:26:48 Step 6/9 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 55cac8451e2f build 30-May-2019 23:26:48 Step 7/9 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 508f78486461 build 30-May-2019 23:26:48 Step 8/9 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> f5d1282df646 build 30-May-2019 23:26:48 Step 9/9 : CMD python -c "from simple_extractor import SimplePythonExtractor; from ${EXTRACTION_MODULE} import *; SimplePythonExtractor(${EXTRACTION_FUNC}).start()" build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> c6fdc7456e56 build 30-May-2019 23:26:48 [Warning] One or more build-args [PYTHON_VERSION] were not consumed build 30-May-2019 23:26:48 Successfully built c6fdc7456e56 build 30-May-2019 23:26:48 Successfully tagged clowder/extractors-simple-extractor-python3:onbuild build 30-May-2019 23:26:48 Sending build context to Docker daemon 13.31kB build 30-May-2019 23:26:48 build 30-May-2019 23:26:48 Step 1/10 : FROM clowder/pyclowder:latest build 30-May-2019 23:26:48 ---> e3941ef228e0 build 30-May-2019 23:26:48 Step 2/10 : ENV R_SCRIPT="" R_FUNCTION="" build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 4b8f93c5517d build 30-May-2019 23:26:48 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 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 2d3760fa8fb4 build 30-May-2019 23:26:48 Step 4/10 : COPY r_extractor.py launcher.R /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 6989934b3b5d build 30-May-2019 23:26:48 Step 5/10 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> d0e5a7a64f6f build 30-May-2019 23:26:48 Step 6/10 : 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 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 005a099d3f4a build 30-May-2019 23:26:48 Step 7/10 : ONBUILD COPY docker.R* Dockerfile /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 7cc834a1f567 build 30-May-2019 23:26:48 Step 8/10 : ONBUILD RUN if [ -e docker.R ]; then Rscript docker.R; fi build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 634c6259d143 build 30-May-2019 23:26:48 Step 9/10 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> a3d77f40c658 build 30-May-2019 23:26:48 Step 10/10 : CMD python r_extractor.py build 30-May-2019 23:26:48 ---> Using cache build 30-May-2019 23:26:48 ---> 4a56839e2505 build 30-May-2019 23:26:48 [Warning] One or more build-args [PYTHON_VERSION] were not consumed build 30-May-2019 23:26:48 Successfully built 4a56839e2505 build 30-May-2019 23:26:48 Successfully tagged clowder/extractors-simple-r-extractor-python3:onbuild build 30-May-2019 23:26:48 Sending build context to Docker daemon 9.216kB build 30-May-2019 23:26:48 build 30-May-2019 23:26:48 Step 1/2 : FROM clowder/pyclowder:onbuild build 30-May-2019 23:26:48 # Executing 5 build triggers build 30-May-2019 23:26:49 ---> Running in 9c1763770952 build 30-May-2019 23:26:51 Removing intermediate container 9c1763770952 build 30-May-2019 23:26:51 ---> Running in 4d5ae29e14dc build 30-May-2019 23:26:54 Removing intermediate container 4d5ae29e14dc build 30-May-2019 23:26:54 ---> e788ad81d386 build 30-May-2019 23:26:54 Step 2/2 : ENV MAIN_SCRIPT="wordcount.py" build 30-May-2019 23:26:54 ---> Running in 2e7e6c021b7a build 30-May-2019 23:26:55 Removing intermediate container 2e7e6c021b7a build 30-May-2019 23:26:55 ---> e27f64ef2964 build 30-May-2019 23:26:55 Successfully built e27f64ef2964 build 30-May-2019 23:26:55 Successfully tagged clowder/extractors-wordcount:latest build 30-May-2019 23:26:55 Sending build context to Docker daemon 5.12kB build 30-May-2019 23:26:55 build 30-May-2019 23:26:55 Step 1/3 : FROM clowder/extractors-simple-extractor:onbuild build 30-May-2019 23:26:55 # Executing 5 build triggers build 30-May-2019 23:26:55 ---> Running in 30d7573b0256 build 30-May-2019 23:26:58 Removing intermediate container 30d7573b0256 build 30-May-2019 23:26:58 ---> Running in 4ae3509dc8a4 build 30-May-2019 23:27:00 Removing intermediate container 4ae3509dc8a4 build 30-May-2019 23:27:00 ---> 522da0dcdafe build 30-May-2019 23:27:00 Step 2/3 : ENV EXTRACTION_FUNC="wordcount" build 30-May-2019 23:27:01 ---> Running in 6e28bfe25db4 build 30-May-2019 23:27:01 Removing intermediate container 6e28bfe25db4 build 30-May-2019 23:27:01 ---> 516a66493328 build 30-May-2019 23:27:01 Step 3/3 : ENV EXTRACTION_MODULE="wordcount" build 30-May-2019 23:27:01 ---> Running in 278925a6a8c9 build 30-May-2019 23:27:02 Removing intermediate container 278925a6a8c9 build 30-May-2019 23:27:02 ---> 468500054fc3 build 30-May-2019 23:27:02 Successfully built 468500054fc3 build 30-May-2019 23:27:02 Successfully tagged clowder/extractors-wordcount-simple-extractor:latest build 30-May-2019 23:27:02 Sending build context to Docker daemon 5.12kB build 30-May-2019 23:27:02 build 30-May-2019 23:27:02 Step 1/2 : FROM clowder/extractors-simple-r-extractor:onbuild build 30-May-2019 23:27:02 # Executing 5 build triggers build 30-May-2019 23:27:03 ---> Running in 12288a4c36b3 build 30-May-2019 23:27:04 Removing intermediate container 12288a4c36b3 build 30-May-2019 23:27:05 ---> Running in c13c669af331 build 30-May-2019 23:27:07 Removing intermediate container c13c669af331 build 30-May-2019 23:27:07 ---> e0c4a7b48e6b build 30-May-2019 23:27:07 Step 2/2 : ENV R_SCRIPT="wordcount.R" R_FUNCTION="process_file" build 30-May-2019 23:27:07 ---> Running in 38e193733fea build 30-May-2019 23:27:08 Removing intermediate container 38e193733fea build 30-May-2019 23:27:08 ---> 7d13c83a3f92 build 30-May-2019 23:27:08 Successfully built 7d13c83a3f92 build 30-May-2019 23:27:08 Successfully tagged clowder/extractors-wordcount-simple-r-extractor:latest build 30-May-2019 23:27:08 Sending build context to Docker daemon 8.192kB build 30-May-2019 23:27:08 build 30-May-2019 23:27:08 Step 1/7 : FROM python:3.5 build 30-May-2019 23:27:08 ---> 74a0040526f9 build 30-May-2019 23:27:08 Step 2/7 : ENV RABBITMQ_URI="amqp://guest:guest@rabbitmq/%2F" build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> 5a32a85f447e build 30-May-2019 23:27:08 Step 3/7 : EXPOSE 9999 build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> 337a1aeaf454 build 30-May-2019 23:27:08 Step 4/7 : RUN pip install pika==0.11.2 requests==2.18.4 build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> ed000a685d11 build 30-May-2019 23:27:08 Step 5/7 : WORKDIR /src build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> 53923ce19092 build 30-May-2019 23:27:08 Step 6/7 : COPY monitor.py /src/ build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> 7b6191bf8e92 build 30-May-2019 23:27:08 Step 7/7 : CMD python monitor.py build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> e292e6c4f2e2 build 30-May-2019 23:27:08 Successfully built e292e6c4f2e2 build 30-May-2019 23:27:08 Successfully tagged clowder/extractors-monitor:latest simple 30-May-2019 23:27:08 Finished task 'docker build' with result: Success simple 30-May-2019 23:27:08 Starting task 'docker push' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 30-May-2019 23:27:08 Beginning to execute external process for build 'Clowder - pyclowder2 - bugfix-BD-2345-open-extractor-info-json-with-utf-8-encoding - Default Job #2 (CATS-PYC299-JOB1-2)'\n ... running command line: \n/bin/sh release.sh\n ... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding\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-2345-open-extractor-info-json-with-utf-8-encoding\nbamboo_repository_revision_number=a54e1410f4217209bc72e2af5b2266ead7d08a0d\nbamboo_resultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PYC299-JOB1-2\nbamboo_capability_system_builder_command_sphinx=/usr/bin/sphinx-build\nbamboo_repository_170524726_branch_name=bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding\nbamboo_build_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1\nbamboo_planRepository_1_name=pyclowder2\nbamboo_buildKey=CATS-PYC299-JOB1\nbamboo_capability_system_os=linux\nbamboo_shortPlanName=bugfix-BD-2345-open-extractor-info-json-with-utf-8-encoding\nbamboo_repository_170524726_previous_revision_number=8c97747b1d0882a0524eb5885c4f82791a45c25d\nbamboo_planRepository_name=pyclowder2\nbamboo_repository_170524726_git_username=\nbamboo_buildNumber=2\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-PYC299-JOB1-2\nbamboo_planRepository_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder2.git\nbamboo_agentId=143032321\nbamboo_planName=Clowder - pyclowder2 - bugfix-BD-2345-open-extractor-info-json-with-utf-8-encoding\nbamboo_build_commandline_com_atlassian_bamboo_plugins_scripttask_task_builder_script_6=/home/bamboo/bamboo-agent-home/temp/CATS-PYC299-JOB1-2-ScriptBuildTask-9012133832384737066.sh\nbamboo_shortPlanKey=PYC299\nbamboo_capability_system_builder_command_sbt_0_13=/home/bamboo/sbt-0.13.2/bin/sbt\nbamboo_capability_system_builder_node_Node_js_v0_10_28=/home/bamboo/node-v0.10.28/bin/node\nbamboo_shortJobKey=JOB1\nbamboo_planRepository_revision=a54e1410f4217209bc72e2af5b2266ead7d08a0d\nbamboo_buildTimeStamp=2019-05-30T23:21:47.421-05:00\nbamboo_repository_previous_revision_number=8c97747b1d0882a0524eb5885c4f82791a45c25d\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_build_commandline_com_atlassian_bamboo_plugins_scripttask_task_builder_script_3=/home/bamboo/bamboo-agent-home/temp/CATS-PYC299-JOB1-2-ScriptBuildTask-3919310685512841381.sh\nbamboo_planRepository_previousRevision=8c97747b1d0882a0524eb5885c4f82791a45c25d\nbamboo_build_commandline_com_atlassian_bamboo_plugins_scripttask_task_builder_script_2=/bin/sh docker.sh\nbamboo_repository_170524726_revision_number=a54e1410f4217209bc72e2af5b2266ead7d08a0d\nbamboo_repository_git_branch=bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding\nbamboo_buildResultKey=CATS-PYC299-JOB1-2\nbamboo_repository_branch_name=bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding\nbamboo_buildPlanName=Clowder - pyclowder2 - bugfix-BD-2345-open-extractor-info-json-with-utf-8-encoding - Default Job\nbamboo_planRepository_1_revision=a54e1410f4217209bc72e2af5b2266ead7d08a0d\nbamboo_capability_system_builder_command_python3=/usr/bin/python3\nbamboo_repository_170524726_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder2.git\nbamboo_repository_name=pyclowder2\nbamboo_repository_170524726_name=pyclowder2\nbamboo_repository_170524726_git_branch=bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding\nbamboo_buildFailed=false\nbamboo_capability_system_docker_executable=/usr/bin/docker\nbamboo_capability_system_builder_command_grunt=/home/bamboo/node-v0.10.28/bin/grunt\nbamboo_planRepository_branch=bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding\nbamboo_agentWorkingDirectory=/home/bamboo/bamboo-agent-home/xml-data/build-dir\nbamboo_capability_system_git_executable=/usr/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=8c97747b1d0882a0524eb5885c4f82791a45c25d\nbamboo_capability_system_builder_sbt_SBT_0_13_13=/home/bamboo/sbt-0.13.13\nbamboo_planRepository_branchDisplayName=bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding\nbamboo_capability_system_builder_command_phantomjs=/home/bamboo/phantomjs-1.9.8/bin/phantomjs\nbamboo_planRepository_1_type=bbserver\nbamboo_planRepository_branchName=bugfix/BD-2345-open-extractor-info-json-with-utf-8-encoding\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-170328171\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/pyclowder2.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-PYC299-JOB1\nbamboo_planKey=CATS-PYC299\nbamboo_planRepository_1_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder2.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-2345-open-extractor-info-json-with-utf-8-encoding\n build 30-May-2019 23:27:08 Sending build context to Docker daemon 281.1kB build 30-May-2019 23:27:08 build 30-May-2019 23:27:08 Step 1/9 : FROM ubuntu:16.04 build 30-May-2019 23:27:08 ---> 2a697363a870 build 30-May-2019 23:27:08 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 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> 07339c96c1a7 build 30-May-2019 23:27:08 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 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> 66b8b13e8095 build 30-May-2019 23:27:08 Step 4/9 : COPY pyclowder /tmp/pyclowder/pyclowder build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> d8c1b0c331b0 build 30-May-2019 23:27:08 Step 5/9 : COPY setup.py description.rst /tmp/pyclowder/ build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> 53f00a224aaa build 30-May-2019 23:27:08 Step 6/9 : RUN pip install --upgrade /tmp/pyclowder && rm -rf /tmp/pyclowder build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> eee101981043 build 30-May-2019 23:27:08 Step 7/9 : WORKDIR /home/clowder build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> c91f4b8f86bc build 30-May-2019 23:27:08 Step 8/9 : COPY notifications.json /home/clowder build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> dbc4c8fabc3a build 30-May-2019 23:27:08 Step 9/9 : CMD python "./${MAIN_SCRIPT}" build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> e3941ef228e0 build 30-May-2019 23:27:08 Successfully built e3941ef228e0 build 30-May-2019 23:27:08 Successfully tagged clowder/pyclowder:latest build 30-May-2019 23:27:08 Sending build context to Docker daemon 279.6kB build 30-May-2019 23:27:08 build 30-May-2019 23:27:08 Step 1/6 : FROM clowder/pyclowder build 30-May-2019 23:27:08 ---> e3941ef228e0 build 30-May-2019 23:27:08 Step 2/6 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> b373d4266138 build 30-May-2019 23:27:08 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 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> 8fd45ef39137 build 30-May-2019 23:27:08 Step 4/6 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> c483dc4e92f2 build 30-May-2019 23:27:08 Step 5/6 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> d19ae6315361 build 30-May-2019 23:27:08 Step 6/6 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:27:08 ---> Using cache build 30-May-2019 23:27:08 ---> 826af52f4fb4 build 30-May-2019 23:27:08 Successfully built 826af52f4fb4 build 30-May-2019 23:27:09 Successfully tagged clowder/pyclowder:onbuild build 30-May-2019 23:27:09 Sending build context to Docker daemon 12.8kB build 30-May-2019 23:27:09 build 30-May-2019 23:27:09 Step 1/5 : FROM clowder/pyclowder:onbuild build 30-May-2019 23:27:09 # Executing 5 build triggers build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 1b2b7fc9f69e build 30-May-2019 23:27:09 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 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 24756082800c build 30-May-2019 23:27:09 Step 3/5 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> f536f83844cf build 30-May-2019 23:27:09 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 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> e26084fcad02 build 30-May-2019 23:27:09 Step 5/5 : ONBUILD COPY extractor_info.json /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 2dfbb5176899 build 30-May-2019 23:27:09 Successfully built 2dfbb5176899 build 30-May-2019 23:27:09 Successfully tagged clowder/extractors-binary-preview:onbuild build 30-May-2019 23:27:09 Sending build context to Docker daemon 6.656kB build 30-May-2019 23:27:09 build 30-May-2019 23:27:09 Step 1/9 : FROM clowder/pyclowder:onbuild build 30-May-2019 23:27:09 # Executing 5 build triggers build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 86ff6d69b221 build 30-May-2019 23:27:09 Step 2/9 : ENV EXTRACTION_FUNC="" build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> af366a91ccdd build 30-May-2019 23:27:09 Step 3/9 : ENV EXTRACTION_MODULE="" build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 5ccb678d30c6 build 30-May-2019 23:27:09 Step 4/9 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 5508388d0713 build 30-May-2019 23:27:09 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 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> a015d01ce7f7 build 30-May-2019 23:27:09 Step 6/9 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 55cac8451e2f build 30-May-2019 23:27:09 Step 7/9 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 508f78486461 build 30-May-2019 23:27:09 Step 8/9 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> f5d1282df646 build 30-May-2019 23:27:09 Step 9/9 : CMD python -c "from simple_extractor import SimplePythonExtractor; from ${EXTRACTION_MODULE} import *; SimplePythonExtractor(${EXTRACTION_FUNC}).start()" build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> c6fdc7456e56 build 30-May-2019 23:27:09 Successfully built c6fdc7456e56 build 30-May-2019 23:27:09 Successfully tagged clowder/extractors-simple-extractor:onbuild build 30-May-2019 23:27:09 Sending build context to Docker daemon 13.31kB build 30-May-2019 23:27:09 build 30-May-2019 23:27:09 Step 1/10 : FROM clowder/pyclowder:latest build 30-May-2019 23:27:09 ---> e3941ef228e0 build 30-May-2019 23:27:09 Step 2/10 : ENV R_SCRIPT="" R_FUNCTION="" build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 4b8f93c5517d build 30-May-2019 23:27:09 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 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 2d3760fa8fb4 build 30-May-2019 23:27:09 Step 4/10 : COPY r_extractor.py launcher.R /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 6989934b3b5d build 30-May-2019 23:27:09 Step 5/10 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> d0e5a7a64f6f build 30-May-2019 23:27:09 Step 6/10 : 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 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 005a099d3f4a build 30-May-2019 23:27:09 Step 7/10 : ONBUILD COPY docker.R* Dockerfile /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 7cc834a1f567 build 30-May-2019 23:27:09 Step 8/10 : ONBUILD RUN if [ -e docker.R ]; then Rscript docker.R; fi build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 634c6259d143 build 30-May-2019 23:27:09 Step 9/10 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> a3d77f40c658 build 30-May-2019 23:27:09 Step 10/10 : CMD python r_extractor.py build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 4a56839e2505 build 30-May-2019 23:27:09 Successfully built 4a56839e2505 build 30-May-2019 23:27:09 Successfully tagged clowder/extractors-simple-r-extractor:onbuild build 30-May-2019 23:27:09 Sending build context to Docker daemon 281.1kB build 30-May-2019 23:27:09 build 30-May-2019 23:27:09 Step 1/9 : FROM ubuntu:16.04 build 30-May-2019 23:27:09 ---> 2a697363a870 build 30-May-2019 23:27:09 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 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 07339c96c1a7 build 30-May-2019 23:27:09 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 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 66b8b13e8095 build 30-May-2019 23:27:09 Step 4/9 : COPY pyclowder /tmp/pyclowder/pyclowder build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> d8c1b0c331b0 build 30-May-2019 23:27:09 Step 5/9 : COPY setup.py description.rst /tmp/pyclowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 53f00a224aaa build 30-May-2019 23:27:09 Step 6/9 : RUN pip install --upgrade /tmp/pyclowder && rm -rf /tmp/pyclowder build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> eee101981043 build 30-May-2019 23:27:09 Step 7/9 : WORKDIR /home/clowder build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> c91f4b8f86bc build 30-May-2019 23:27:09 Step 8/9 : COPY notifications.json /home/clowder build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> dbc4c8fabc3a build 30-May-2019 23:27:09 Step 9/9 : CMD python "./${MAIN_SCRIPT}" build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> e3941ef228e0 build 30-May-2019 23:27:09 [Warning] One or more build-args [PYTHON_VERSION] were not consumed build 30-May-2019 23:27:09 Successfully built e3941ef228e0 build 30-May-2019 23:27:09 Successfully tagged clowder/pyclowder-python3:latest build 30-May-2019 23:27:09 Sending build context to Docker daemon 279.6kB build 30-May-2019 23:27:09 build 30-May-2019 23:27:09 Step 1/6 : FROM clowder/pyclowder build 30-May-2019 23:27:09 ---> e3941ef228e0 build 30-May-2019 23:27:09 Step 2/6 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> b373d4266138 build 30-May-2019 23:27:09 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 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 8fd45ef39137 build 30-May-2019 23:27:09 Step 4/6 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> c483dc4e92f2 build 30-May-2019 23:27:09 Step 5/6 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> d19ae6315361 build 30-May-2019 23:27:09 Step 6/6 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:27:09 ---> Using cache build 30-May-2019 23:27:09 ---> 826af52f4fb4 build 30-May-2019 23:27:09 [Warning] One or more build-args [PYTHON_VERSION] were not consumed build 30-May-2019 23:27:09 Successfully built 826af52f4fb4 build 30-May-2019 23:27:09 Successfully tagged clowder/pyclowder-python3:onbuild build 30-May-2019 23:27:09 Sending build context to Docker daemon 6.656kB build 30-May-2019 23:27:09 build 30-May-2019 23:27:10 Step 1/9 : FROM clowder/pyclowder:onbuild build 30-May-2019 23:27:10 # Executing 5 build triggers build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 86ff6d69b221 build 30-May-2019 23:27:10 Step 2/9 : ENV EXTRACTION_FUNC="" build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> af366a91ccdd build 30-May-2019 23:27:10 Step 3/9 : ENV EXTRACTION_MODULE="" build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 5ccb678d30c6 build 30-May-2019 23:27:10 Step 4/9 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 5508388d0713 build 30-May-2019 23:27:10 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 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> a015d01ce7f7 build 30-May-2019 23:27:10 Step 6/9 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/ build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 55cac8451e2f build 30-May-2019 23:27:10 Step 7/9 : ONBUILD RUN if [ -e requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 508f78486461 build 30-May-2019 23:27:10 Step 8/9 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> f5d1282df646 build 30-May-2019 23:27:10 Step 9/9 : CMD python -c "from simple_extractor import SimplePythonExtractor; from ${EXTRACTION_MODULE} import *; SimplePythonExtractor(${EXTRACTION_FUNC}).start()" build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> c6fdc7456e56 build 30-May-2019 23:27:10 [Warning] One or more build-args [PYTHON_VERSION] were not consumed build 30-May-2019 23:27:10 Successfully built c6fdc7456e56 build 30-May-2019 23:27:10 Successfully tagged clowder/extractors-simple-extractor-python3:onbuild build 30-May-2019 23:27:10 Sending build context to Docker daemon 13.31kB build 30-May-2019 23:27:10 build 30-May-2019 23:27:10 Step 1/10 : FROM clowder/pyclowder:latest build 30-May-2019 23:27:10 ---> e3941ef228e0 build 30-May-2019 23:27:10 Step 2/10 : ENV R_SCRIPT="" R_FUNCTION="" build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 4b8f93c5517d build 30-May-2019 23:27:10 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 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 2d3760fa8fb4 build 30-May-2019 23:27:10 Step 4/10 : COPY r_extractor.py launcher.R /home/clowder/ build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 6989934b3b5d build 30-May-2019 23:27:10 Step 5/10 : ONBUILD COPY packages.* Dockerfile /home/clowder/ build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> d0e5a7a64f6f build 30-May-2019 23:27:10 Step 6/10 : 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 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 005a099d3f4a build 30-May-2019 23:27:10 Step 7/10 : ONBUILD COPY docker.R* Dockerfile /home/clowder/ build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 7cc834a1f567 build 30-May-2019 23:27:10 Step 8/10 : ONBUILD RUN if [ -e docker.R ]; then Rscript docker.R; fi build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 634c6259d143 build 30-May-2019 23:27:10 Step 9/10 : ONBUILD ADD . /home/clowder/ build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> a3d77f40c658 build 30-May-2019 23:27:10 Step 10/10 : CMD python r_extractor.py build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 4a56839e2505 build 30-May-2019 23:27:10 [Warning] One or more build-args [PYTHON_VERSION] were not consumed build 30-May-2019 23:27:10 Successfully built 4a56839e2505 build 30-May-2019 23:27:10 Successfully tagged clowder/extractors-simple-r-extractor-python3:onbuild build 30-May-2019 23:27:10 Sending build context to Docker daemon 9.216kB build 30-May-2019 23:27:10 build 30-May-2019 23:27:10 Step 1/2 : FROM clowder/pyclowder:onbuild build 30-May-2019 23:27:10 # Executing 5 build triggers build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> e788ad81d386 build 30-May-2019 23:27:10 Step 2/2 : ENV MAIN_SCRIPT="wordcount.py" build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> e27f64ef2964 build 30-May-2019 23:27:10 Successfully built e27f64ef2964 build 30-May-2019 23:27:10 Successfully tagged clowder/extractors-wordcount:latest build 30-May-2019 23:27:10 Sending build context to Docker daemon 5.12kB build 30-May-2019 23:27:10 build 30-May-2019 23:27:10 Step 1/3 : FROM clowder/extractors-simple-extractor:onbuild build 30-May-2019 23:27:10 # Executing 5 build triggers build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 522da0dcdafe build 30-May-2019 23:27:10 Step 2/3 : ENV EXTRACTION_FUNC="wordcount" build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 516a66493328 build 30-May-2019 23:27:10 Step 3/3 : ENV EXTRACTION_MODULE="wordcount" build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 468500054fc3 build 30-May-2019 23:27:10 Successfully built 468500054fc3 build 30-May-2019 23:27:10 Successfully tagged clowder/extractors-wordcount-simple-extractor:latest build 30-May-2019 23:27:10 Sending build context to Docker daemon 5.12kB build 30-May-2019 23:27:10 build 30-May-2019 23:27:10 Step 1/2 : FROM clowder/extractors-simple-r-extractor:onbuild build 30-May-2019 23:27:10 # Executing 5 build triggers build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> e0c4a7b48e6b build 30-May-2019 23:27:10 Step 2/2 : ENV R_SCRIPT="wordcount.R" R_FUNCTION="process_file" build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 7d13c83a3f92 build 30-May-2019 23:27:10 Successfully built 7d13c83a3f92 build 30-May-2019 23:27:10 Successfully tagged clowder/extractors-wordcount-simple-r-extractor:latest build 30-May-2019 23:27:10 Sending build context to Docker daemon 8.192kB build 30-May-2019 23:27:10 build 30-May-2019 23:27:10 Step 1/7 : FROM python:3.5 build 30-May-2019 23:27:10 ---> 74a0040526f9 build 30-May-2019 23:27:10 Step 2/7 : ENV RABBITMQ_URI="amqp://guest:guest@rabbitmq/%2F" build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 5a32a85f447e build 30-May-2019 23:27:10 Step 3/7 : EXPOSE 9999 build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 337a1aeaf454 build 30-May-2019 23:27:10 Step 4/7 : RUN pip install pika==0.11.2 requests==2.18.4 build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> ed000a685d11 build 30-May-2019 23:27:10 Step 5/7 : WORKDIR /src build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 53923ce19092 build 30-May-2019 23:27:10 Step 6/7 : COPY monitor.py /src/ build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> 7b6191bf8e92 build 30-May-2019 23:27:10 Step 7/7 : CMD python monitor.py build 30-May-2019 23:27:10 ---> Using cache build 30-May-2019 23:27:10 ---> e292e6c4f2e2 build 30-May-2019 23:27:10 Successfully built e292e6c4f2e2 build 30-May-2019 23:27:10 Successfully tagged clowder/extractors-monitor:latest simple 30-May-2019 23:27:10 Finished task 'docker push' with result: Success simple 30-May-2019 23:27:10 Starting task 'test results' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.junit' simple 30-May-2019 23:27:10 Parsing test results under /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC299-JOB1... simple 30-May-2019 23:27:10 Finished task 'test results' with result: Success simple 30-May-2019 23:27:10 Running post build plugin 'Docker Container Cleanup' simple 30-May-2019 23:27:10 Running post build plugin 'NCover Results Collector' simple 30-May-2019 23:27:10 Running post build plugin 'Clover Results Collector' simple 30-May-2019 23:27:10 Running post build plugin 'npm Cache Cleanup' simple 30-May-2019 23:27:10 Running post build plugin 'Artifact Copier' simple 30-May-2019 23:27:10 Finalising the build... simple 30-May-2019 23:27:10 Stopping timer. simple 30-May-2019 23:27:10 Build CATS-PYC299-JOB1-2 completed. simple 30-May-2019 23:27:11 Running on server: post build plugin 'NCover Results Collector' simple 30-May-2019 23:27:11 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 30-May-2019 23:27:11 Running on server: post build plugin 'Clover Delta Calculator' simple 30-May-2019 23:27:11 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 30-May-2019 23:27:11 All post build plugins have finished simple 30-May-2019 23:27:11 Generating build results summary... simple 30-May-2019 23:27:11 Saving build results to disk... simple 30-May-2019 23:27:11 Logging substituted variables... simple 30-May-2019 23:27:11 Indexing build results... simple 30-May-2019 23:27:11 Finished building CATS-PYC299-JOB1-2.