Next Generation of pyClowder

Build: #1 was successful

Job: Default Job was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 3,927 lines of output.The output is too long and has been truncated to the last 1,000 lines. Download or view full build log.

01-Dec-2019 07:43:33 Preparing to unpack .../libgfortran3_5.4.0-6ubuntu1~16.04.12_amd64.deb ...
01-Dec-2019 07:43:33 Unpacking libgfortran3:amd64 (5.4.0-6ubuntu1~16.04.12) ...
01-Dec-2019 07:43:33 Selecting previously unselected package libgfortran-5-dev:amd64.
01-Dec-2019 07:43:33 Preparing to unpack .../libgfortran-5-dev_5.4.0-6ubuntu1~16.04.12_amd64.deb ...
01-Dec-2019 07:43:33 Unpacking libgfortran-5-dev:amd64 (5.4.0-6ubuntu1~16.04.12) ...
01-Dec-2019 07:43:34 Selecting previously unselected package gfortran-5.
01-Dec-2019 07:43:34 Preparing to unpack .../gfortran-5_5.4.0-6ubuntu1~16.04.12_amd64.deb ...
01-Dec-2019 07:43:34 Unpacking gfortran-5 (5.4.0-6ubuntu1~16.04.12) ...
01-Dec-2019 07:43:35 Selecting previously unselected package gfortran.
01-Dec-2019 07:43:35 Preparing to unpack .../gfortran_4%3a5.3.1-1ubuntu1_amd64.deb ...
01-Dec-2019 07:43:35 Unpacking gfortran (4:5.3.1-1ubuntu1) ...
01-Dec-2019 07:43:36 Selecting previously unselected package icu-devtools.
01-Dec-2019 07:43:36 Preparing to unpack .../icu-devtools_55.1-7ubuntu0.4_amd64.deb ...
01-Dec-2019 07:43:36 Unpacking icu-devtools (55.1-7ubuntu0.4) ...
01-Dec-2019 07:43:36 Selecting previously unselected package libblas-common.
01-Dec-2019 07:43:36 Preparing to unpack .../libblas-common_3.6.0-2ubuntu2_amd64.deb ...
01-Dec-2019 07:43:36 Unpacking libblas-common (3.6.0-2ubuntu2) ...
01-Dec-2019 07:43:36 Selecting previously unselected package libblas3.
01-Dec-2019 07:43:36 Preparing to unpack .../libblas3_3.6.0-2ubuntu2_amd64.deb ...
01-Dec-2019 07:43:36 Unpacking libblas3 (3.6.0-2ubuntu2) ...
01-Dec-2019 07:43:37 Selecting previously unselected package libblas-dev.
01-Dec-2019 07:43:37 Preparing to unpack .../libblas-dev_3.6.0-2ubuntu2_amd64.deb ...
01-Dec-2019 07:43:37 Unpacking libblas-dev (3.6.0-2ubuntu2) ...
01-Dec-2019 07:43:38 Selecting previously unselected package libbz2-dev:amd64.
01-Dec-2019 07:43:38 Preparing to unpack .../libbz2-dev_1.0.6-8ubuntu0.2_amd64.deb ...
01-Dec-2019 07:43:38 Unpacking libbz2-dev:amd64 (1.0.6-8ubuntu0.2) ...
01-Dec-2019 07:43:38 Selecting previously unselected package libpixman-1-0:amd64.
01-Dec-2019 07:43:38 Preparing to unpack .../libpixman-1-0_0.33.6-1_amd64.deb ...
01-Dec-2019 07:43:38 Unpacking libpixman-1-0:amd64 (0.33.6-1) ...
01-Dec-2019 07:43:38 Selecting previously unselected package libxcb-render0:amd64.
01-Dec-2019 07:43:38 Preparing to unpack .../libxcb-render0_1.11.1-1ubuntu1_amd64.deb ...
01-Dec-2019 07:43:38 Unpacking libxcb-render0:amd64 (1.11.1-1ubuntu1) ...
01-Dec-2019 07:43:39 Selecting previously unselected package libxcb-shm0:amd64.
01-Dec-2019 07:43:39 Preparing to unpack .../libxcb-shm0_1.11.1-1ubuntu1_amd64.deb ...
01-Dec-2019 07:43:39 Unpacking libxcb-shm0:amd64 (1.11.1-1ubuntu1) ...
01-Dec-2019 07:43:39 Selecting previously unselected package libcairo2:amd64.
01-Dec-2019 07:43:39 Preparing to unpack .../libcairo2_1.14.6-1_amd64.deb ...
01-Dec-2019 07:43:39 Unpacking libcairo2:amd64 (1.14.6-1) ...
01-Dec-2019 07:43:40 Selecting previously unselected package libcurl3:amd64.
01-Dec-2019 07:43:40 Preparing to unpack .../libcurl3_7.47.0-1ubuntu2.14_amd64.deb ...
01-Dec-2019 07:43:40 Unpacking libcurl3:amd64 (7.47.0-1ubuntu2.14) ...
01-Dec-2019 07:43:40 Selecting previously unselected package libdatrie1:amd64.
01-Dec-2019 07:43:40 Preparing to unpack .../libdatrie1_0.2.10-2_amd64.deb ...
01-Dec-2019 07:43:40 Unpacking libdatrie1:amd64 (0.2.10-2) ...
01-Dec-2019 07:43:40 Selecting previously unselected package libgraphite2-3:amd64.
01-Dec-2019 07:43:40 Preparing to unpack .../libgraphite2-3_1.3.10-0ubuntu0.16.04.1_amd64.deb ...
01-Dec-2019 07:43:40 Unpacking libgraphite2-3:amd64 (1.3.10-0ubuntu0.16.04.1) ...
01-Dec-2019 07:43:41 Selecting previously unselected package libharfbuzz0b:amd64.
01-Dec-2019 07:43:41 Preparing to unpack .../libharfbuzz0b_1.0.1-1ubuntu0.1_amd64.deb ...
01-Dec-2019 07:43:41 Unpacking libharfbuzz0b:amd64 (1.0.1-1ubuntu0.1) ...
01-Dec-2019 07:43:41 Selecting previously unselected package libicu-dev:amd64.
01-Dec-2019 07:43:41 Preparing to unpack .../libicu-dev_55.1-7ubuntu0.4_amd64.deb ...
01-Dec-2019 07:43:41 Unpacking libicu-dev:amd64 (55.1-7ubuntu0.4) ...
01-Dec-2019 07:43:44 Selecting previously unselected package libjpeg-turbo8-dev:amd64.
01-Dec-2019 07:43:44 Preparing to unpack .../libjpeg-turbo8-dev_1.4.2-0ubuntu3.3_amd64.deb ...
01-Dec-2019 07:43:44 Unpacking libjpeg-turbo8-dev:amd64 (1.4.2-0ubuntu3.3) ...
01-Dec-2019 07:43:44 Selecting previously unselected package libjpeg8:amd64.
01-Dec-2019 07:43:44 Preparing to unpack .../libjpeg8_8c-2ubuntu8_amd64.deb ...
01-Dec-2019 07:43:44 Unpacking libjpeg8:amd64 (8c-2ubuntu8) ...
01-Dec-2019 07:43:44 Selecting previously unselected package libjpeg8-dev:amd64.
01-Dec-2019 07:43:44 Preparing to unpack .../libjpeg8-dev_8c-2ubuntu8_amd64.deb ...
01-Dec-2019 07:43:44 Unpacking libjpeg8-dev:amd64 (8c-2ubuntu8) ...
01-Dec-2019 07:43:45 Selecting previously unselected package libjpeg-dev:amd64.
01-Dec-2019 07:43:45 Preparing to unpack .../libjpeg-dev_8c-2ubuntu8_amd64.deb ...
01-Dec-2019 07:43:45 Unpacking libjpeg-dev:amd64 (8c-2ubuntu8) ...
01-Dec-2019 07:43:45 Selecting previously unselected package liblapack3.
01-Dec-2019 07:43:45 Preparing to unpack .../liblapack3_3.6.0-2ubuntu2_amd64.deb ...
01-Dec-2019 07:43:45 Unpacking liblapack3 (3.6.0-2ubuntu2) ...
01-Dec-2019 07:43:46 Selecting previously unselected package liblapack-dev.
01-Dec-2019 07:43:46 Preparing to unpack .../liblapack-dev_3.6.0-2ubuntu2_amd64.deb ...
01-Dec-2019 07:43:46 Unpacking liblapack-dev (3.6.0-2ubuntu2) ...
01-Dec-2019 07:43:46 Selecting previously unselected package libtinfo-dev:amd64.
01-Dec-2019 07:43:46 Preparing to unpack .../libtinfo-dev_6.0+20160213-1ubuntu1_amd64.deb ...
01-Dec-2019 07:43:46 Unpacking libtinfo-dev:amd64 (6.0+20160213-1ubuntu1) ...
01-Dec-2019 07:43:47 Selecting previously unselected package libncurses5-dev:amd64.
01-Dec-2019 07:43:47 Preparing to unpack .../libncurses5-dev_6.0+20160213-1ubuntu1_amd64.deb ...
01-Dec-2019 07:43:47 Unpacking libncurses5-dev:amd64 (6.0+20160213-1ubuntu1) ...
01-Dec-2019 07:43:48 Selecting previously unselected package libthai-data.
01-Dec-2019 07:43:48 Preparing to unpack .../libthai-data_0.1.24-2_all.deb ...
01-Dec-2019 07:43:48 Unpacking libthai-data (0.1.24-2) ...
01-Dec-2019 07:43:48 Selecting previously unselected package libthai0:amd64.
01-Dec-2019 07:43:48 Preparing to unpack .../libthai0_0.1.24-2_amd64.deb ...
01-Dec-2019 07:43:48 Unpacking libthai0:amd64 (0.1.24-2) ...
01-Dec-2019 07:43:49 Selecting previously unselected package libpango-1.0-0:amd64.
01-Dec-2019 07:43:49 Preparing to unpack .../libpango-1.0-0_1.38.1-1_amd64.deb ...
01-Dec-2019 07:43:49 Unpacking libpango-1.0-0:amd64 (1.38.1-1) ...
01-Dec-2019 07:43:49 Selecting previously unselected package libpangoft2-1.0-0:amd64.
01-Dec-2019 07:43:49 Preparing to unpack .../libpangoft2-1.0-0_1.38.1-1_amd64.deb ...
01-Dec-2019 07:43:49 Unpacking libpangoft2-1.0-0:amd64 (1.38.1-1) ...
01-Dec-2019 07:43:49 Selecting previously unselected package libpangocairo-1.0-0:amd64.
01-Dec-2019 07:43:49 Preparing to unpack .../libpangocairo-1.0-0_1.38.1-1_amd64.deb ...
01-Dec-2019 07:43:49 Unpacking libpangocairo-1.0-0:amd64 (1.38.1-1) ...
01-Dec-2019 07:43:50 Selecting previously unselected package libpaper1:amd64.
01-Dec-2019 07:43:50 Preparing to unpack .../libpaper1_1.1.24+nmu4ubuntu1_amd64.deb ...
01-Dec-2019 07:43:50 Unpacking libpaper1:amd64 (1.1.24+nmu4ubuntu1) ...
01-Dec-2019 07:43:50 Selecting previously unselected package libpaper-utils.
01-Dec-2019 07:43:50 Preparing to unpack .../libpaper-utils_1.1.24+nmu4ubuntu1_amd64.deb ...
01-Dec-2019 07:43:50 Unpacking libpaper-utils (1.1.24+nmu4ubuntu1) ...
01-Dec-2019 07:43:50 Selecting previously unselected package libpcre16-3:amd64.
01-Dec-2019 07:43:50 Preparing to unpack .../libpcre16-3_2%3a8.38-3.1_amd64.deb ...
01-Dec-2019 07:43:51 Unpacking libpcre16-3:amd64 (2:8.38-3.1) ...
01-Dec-2019 07:43:51 Selecting previously unselected package libpcre32-3:amd64.
01-Dec-2019 07:43:51 Preparing to unpack .../libpcre32-3_2%3a8.38-3.1_amd64.deb ...
01-Dec-2019 07:43:51 Unpacking libpcre32-3:amd64 (2:8.38-3.1) ...
01-Dec-2019 07:43:51 Selecting previously unselected package libpcre3-dev:amd64.
01-Dec-2019 07:43:51 Preparing to unpack .../libpcre3-dev_2%3a8.38-3.1_amd64.deb ...
01-Dec-2019 07:43:51 Unpacking libpcre3-dev:amd64 (2:8.38-3.1) ...
01-Dec-2019 07:43:52 Selecting previously unselected package zlib1g-dev:amd64.
01-Dec-2019 07:43:52 Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2ubuntu4.1_amd64.deb ...
01-Dec-2019 07:43:52 Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2ubuntu4.1) ...
01-Dec-2019 07:43:52 Selecting previously unselected package libpng12-dev:amd64.
01-Dec-2019 07:43:52 Preparing to unpack .../libpng12-dev_1.2.54-1ubuntu1.1_amd64.deb ...
01-Dec-2019 07:43:52 Unpacking libpng12-dev:amd64 (1.2.54-1ubuntu1.1) ...
01-Dec-2019 07:43:52 Selecting previously unselected package libreadline6-dev:amd64.
01-Dec-2019 07:43:52 Preparing to unpack .../libreadline6-dev_6.3-8ubuntu2_amd64.deb ...
01-Dec-2019 07:43:52 Unpacking libreadline6-dev:amd64 (6.3-8ubuntu2) ...
01-Dec-2019 07:43:53 Selecting previously unselected package libreadline-dev:amd64.
01-Dec-2019 07:43:53 Preparing to unpack .../libreadline-dev_6.3-8ubuntu2_amd64.deb ...
01-Dec-2019 07:43:53 Unpacking libreadline-dev:amd64 (6.3-8ubuntu2) ...
01-Dec-2019 07:43:54 Selecting previously unselected package libtcl8.6:amd64.
01-Dec-2019 07:43:54 Preparing to unpack .../libtcl8.6_8.6.5+dfsg-2_amd64.deb ...
01-Dec-2019 07:43:54 Unpacking libtcl8.6:amd64 (8.6.5+dfsg-2) ...
01-Dec-2019 07:43:54 Selecting previously unselected package libtiff5:amd64.
01-Dec-2019 07:43:54 Preparing to unpack .../libtiff5_4.0.6-1ubuntu0.7_amd64.deb ...
01-Dec-2019 07:43:54 Unpacking libtiff5:amd64 (4.0.6-1ubuntu0.7) ...
01-Dec-2019 07:43:55 Selecting previously unselected package libtk8.6:amd64.
01-Dec-2019 07:43:55 Preparing to unpack .../libtk8.6_8.6.5-1_amd64.deb ...
01-Dec-2019 07:43:55 Unpacking libtk8.6:amd64 (8.6.5-1) ...
01-Dec-2019 07:43:55 Selecting previously unselected package libxt6:amd64.
01-Dec-2019 07:43:55 Preparing to unpack .../libxt6_1%3a1.1.5-0ubuntu1_amd64.deb ...
01-Dec-2019 07:43:55 Unpacking libxt6:amd64 (1:1.1.5-0ubuntu1) ...
01-Dec-2019 07:43:56 Selecting previously unselected package pkg-config.
01-Dec-2019 07:43:56 Preparing to unpack .../pkg-config_0.29.1-0ubuntu1_amd64.deb ...
01-Dec-2019 07:43:56 Unpacking pkg-config (0.29.1-0ubuntu1) ...
01-Dec-2019 07:43:56 Selecting previously unselected package zip.
01-Dec-2019 07:43:56 Preparing to unpack .../archives/zip_3.0-11_amd64.deb ...
01-Dec-2019 07:43:56 Unpacking zip (3.0-11) ...
01-Dec-2019 07:43:56 Selecting previously unselected package unzip.
01-Dec-2019 07:43:56 Preparing to unpack .../unzip_6.0-20ubuntu1_amd64.deb ...
01-Dec-2019 07:43:56 Unpacking unzip (6.0-20ubuntu1) ...
01-Dec-2019 07:43:57 Selecting previously unselected package xdg-utils.
01-Dec-2019 07:43:57 Preparing to unpack .../xdg-utils_1.1.1-1ubuntu1.16.04.3_all.deb ...
01-Dec-2019 07:43:57 Unpacking xdg-utils (1.1.1-1ubuntu1.16.04.3) ...
01-Dec-2019 07:43:58 Selecting previously unselected package r-base-core.
01-Dec-2019 07:43:58 Preparing to unpack .../r-base-core_3.4.4-1xenial0_amd64.deb ...
01-Dec-2019 07:43:58 Unpacking r-base-core (3.4.4-1xenial0) ...
01-Dec-2019 07:44:00 Selecting previously unselected package liblzma-dev:amd64.
01-Dec-2019 07:44:00 Preparing to unpack .../liblzma-dev_5.1.1alpha+20120614-2ubuntu2_amd64.deb ...
01-Dec-2019 07:44:00 Unpacking liblzma-dev:amd64 (5.1.1alpha+20120614-2ubuntu2) ...
01-Dec-2019 07:44:01 Selecting previously unselected package r-base-dev.
01-Dec-2019 07:44:01 Preparing to unpack .../r-base-dev_3.4.4-1xenial0_all.deb ...
01-Dec-2019 07:44:01 Unpacking r-base-dev (3.4.4-1xenial0) ...
01-Dec-2019 07:44:01 Processing triggers for libc-bin (2.23-0ubuntu11) ...
01-Dec-2019 07:44:01 Processing triggers for mime-support (3.59ubuntu1) ...
01-Dec-2019 07:44:01 Setting up libgdbm3:amd64 (1.8.3-13.1) ...
01-Dec-2019 07:44:02 Setting up libglib2.0-0:amd64 (2.48.2-0ubuntu4.4) ...
01-Dec-2019 07:44:02 No schema files found: doing nothing.
01-Dec-2019 07:44:02 Setting up libxau6:amd64 (1:1.0.8-1) ...
01-Dec-2019 07:44:02 Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ...
01-Dec-2019 07:44:02 Setting up libxcb1:amd64 (1.11.1-1ubuntu1) ...
01-Dec-2019 07:44:02 Setting up libx11-data (2:1.6.3-1ubuntu2.1) ...
01-Dec-2019 07:44:02 Setting up libx11-6:amd64 (2:1.6.3-1ubuntu2.1) ...
01-Dec-2019 07:44:03 Setting up libxext6:amd64 (2:1.3.3-1) ...
01-Dec-2019 07:44:03 Setting up groff-base (1.22.3-7) ...
01-Dec-2019 07:44:03 Setting up bsdmainutils (9.0.6ubuntu3) ...
01-Dec-2019 07:44:03 update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
01-Dec-2019 07:44:03 update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
01-Dec-2019 07:44:03 Setting up libpipeline1:amd64 (1.4.1-2) ...
01-Dec-2019 07:44:04 Setting up man-db (2.7.5-1) ...
01-Dec-2019 07:44:04 debconf: unable to initialize frontend: Dialog
01-Dec-2019 07:44:04 debconf: (TERM is not set, so the dialog frontend is not usable.)
01-Dec-2019 07:44:04 debconf: falling back to frontend: Readline
01-Dec-2019 07:44:04 Building database of manual pages ...
01-Dec-2019 07:44:12 Setting up fonts-dejavu-core (2.35-1) ...
01-Dec-2019 07:44:13 Setting up ucf (3.0036) ...
01-Dec-2019 07:44:13 debconf: unable to initialize frontend: Dialog
01-Dec-2019 07:44:13 debconf: (TERM is not set, so the dialog frontend is not usable.)
01-Dec-2019 07:44:13 debconf: falling back to frontend: Readline
01-Dec-2019 07:44:13 Setting up fontconfig-config (2.11.94-0ubuntu1.1) ...
01-Dec-2019 07:44:16 Setting up libpng12-0:amd64 (1.2.54-1ubuntu1.1) ...
01-Dec-2019 07:44:16 Setting up libfreetype6:amd64 (2.6.1-0.1ubuntu2.4) ...
01-Dec-2019 07:44:16 Setting up libfontconfig1:amd64 (2.11.94-0ubuntu1.1) ...
01-Dec-2019 07:44:16 Setting up fontconfig (2.11.94-0ubuntu1.1) ...
01-Dec-2019 07:44:18 Regenerating fonts cache... done.
01-Dec-2019 07:44:18 Setting up x11-common (1:7.7+13ubuntu3.1) ...
01-Dec-2019 07:44:19 debconf: unable to initialize frontend: Dialog
01-Dec-2019 07:44:19 debconf: (TERM is not set, so the dialog frontend is not usable.)
01-Dec-2019 07:44:19 debconf: falling back to frontend: Readline
01-Dec-2019 07:44:19 update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
01-Dec-2019 07:44:19 invoke-rc.d: could not determine current runlevel
01-Dec-2019 07:44:19 invoke-rc.d: policy-rc.d denied execution of start.
01-Dec-2019 07:44:19 Setting up libice6:amd64 (2:1.0.9-1) ...
01-Dec-2019 07:44:20 Setting up libjpeg-turbo8:amd64 (1.4.2-0ubuntu3.3) ...
01-Dec-2019 07:44:20 Setting up libpcrecpp0v5:amd64 (2:8.38-3.1) ...
01-Dec-2019 07:44:20 Setting up libsigsegv2:amd64 (2.10-4) ...
01-Dec-2019 07:44:20 Setting up libsm6:amd64 (2:1.2.2-1) ...
01-Dec-2019 07:44:20 Setting up libunistring0:amd64 (0.9.3-5.2ubuntu1) ...
01-Dec-2019 07:44:21 Setting up libxrender1:amd64 (1:0.9.9-0ubuntu1) ...
01-Dec-2019 07:44:21 Setting up libxft2:amd64 (2.3.2-1) ...
01-Dec-2019 07:44:21 Setting up libxss1:amd64 (1:1.2.2-1) ...
01-Dec-2019 07:44:21 Setting up perl-modules-5.22 (5.22.1-9ubuntu0.6) ...
01-Dec-2019 07:44:21 Setting up libperl5.22:amd64 (5.22.1-9ubuntu0.6) ...
01-Dec-2019 07:44:21 Setting up perl (5.22.1-9ubuntu0.6) ...
01-Dec-2019 07:44:22 update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode
01-Dec-2019 07:44:22 Setting up libpython2.7-stdlib:amd64 (2.7.12-1ubuntu0~16.04.9) ...
01-Dec-2019 07:44:22 Setting up python2.7 (2.7.12-1ubuntu0~16.04.9) ...
01-Dec-2019 07:44:23 Setting up libpython-stdlib:amd64 (2.7.12-1~16.04) ...
01-Dec-2019 07:44:23 Setting up python (2.7.12-1~16.04) ...
01-Dec-2019 07:44:24 Setting up libjbig0:amd64 (2.1-3.1) ...
01-Dec-2019 07:44:24 Setting up libmpfr4:amd64 (3.1.4-1) ...
01-Dec-2019 07:44:24 Setting up libmpc3:amd64 (1.0.3-1) ...
01-Dec-2019 07:44:24 Setting up tzdata (2019c-0ubuntu0.16.04) ...
01-Dec-2019 07:44:24 debconf: unable to initialize frontend: Dialog
01-Dec-2019 07:44:24 debconf: (TERM is not set, so the dialog frontend is not usable.)
01-Dec-2019 07:44:24 debconf: falling back to frontend: Readline
01-Dec-2019 07:44:24
01-Dec-2019 07:44:24 Current default time zone: 'Etc/UTC'
01-Dec-2019 07:44:24 Local time is now:      Sun Dec  1 13:44:24 UTC 2019.
01-Dec-2019 07:44:24 Universal Time is now:  Sun Dec  1 13:44:24 UTC 2019.
01-Dec-2019 07:44:24 Run 'dpkg-reconfigure tzdata' if you wish to change it.
01-Dec-2019 07:44:24
01-Dec-2019 07:44:24 Setting up bzip2 (1.0.6-8ubuntu0.2) ...
01-Dec-2019 07:44:25 Setting up libmagic1:amd64 (1:5.25-2ubuntu1.3) ...
01-Dec-2019 07:44:25 Setting up file (1:5.25-2ubuntu1.3) ...
01-Dec-2019 07:44:25 Setting up netbase (5.3) ...
01-Dec-2019 07:44:25 Setting up openssl (1.0.2g-1ubuntu4.15) ...
01-Dec-2019 07:44:25 Setting up ca-certificates (20170717~16.04.2) ...
01-Dec-2019 07:44:26 debconf: unable to initialize frontend: Dialog
01-Dec-2019 07:44:26 debconf: (TERM is not set, so the dialog frontend is not usable.)
01-Dec-2019 07:44:26 debconf: falling back to frontend: Readline
01-Dec-2019 07:44:27 Setting up libasprintf0v5:amd64 (0.19.7-2ubuntu3.1) ...
01-Dec-2019 07:44:27 Setting up gettext-base (0.19.7-2ubuntu3.1) ...
01-Dec-2019 07:44:27 Setting up libicu55:amd64 (55.1-7ubuntu0.4) ...
01-Dec-2019 07:44:27 Setting up libxml2:amd64 (2.9.3+dfsg1-1ubuntu0.6) ...
01-Dec-2019 07:44:28 Setting up libxmuu1:amd64 (2:1.1.2-2) ...
01-Dec-2019 07:44:28 Setting up xauth (1:1.0.9-1ubuntu2) ...
01-Dec-2019 07:44:28 Setting up m4 (1.4.17-5) ...
01-Dec-2019 07:44:28 Setting up autoconf (2.69-9) ...
01-Dec-2019 07:44:28 Setting up autotools-dev (20150820.1) ...
01-Dec-2019 07:44:29 Setting up automake (1:1.15-4ubuntu1) ...
01-Dec-2019 07:44:29 update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
01-Dec-2019 07:44:29 Setting up binutils (2.26.1-1ubuntu1~16.04.8) ...
01-Dec-2019 07:44:29 Setting up libc-dev-bin (2.23-0ubuntu11) ...
01-Dec-2019 07:44:29 Setting up linux-libc-dev:amd64 (4.4.0-169.198) ...
01-Dec-2019 07:44:29 Setting up libc6-dev:amd64 (2.23-0ubuntu11) ...
01-Dec-2019 07:44:29 Setting up libisl15:amd64 (0.16.1-1) ...
01-Dec-2019 07:44:29 Setting up cpp-5 (5.4.0-6ubuntu1~16.04.12) ...
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01-Dec-2019 07:44:54 148 added, 0 removed; done.
01-Dec-2019 07:44:54 Running hooks in /etc/ca-certificates/update.d...
01-Dec-2019 07:44:54 done.
01-Dec-2019 07:44:54 Installing package into '/usr/local/lib/R/site-library'
01-Dec-2019 07:44:54 (as 'lib' is unspecified)
01-Dec-2019 07:44:55 trying URL 'http://cran.rstudio.com/src/contrib/jsonlite_1.6.tar.gz'
01-Dec-2019 07:44:55 Content type 'application/x-gzip' length 1052728 bytes (1.0 MB)
01-Dec-2019 07:44:55 ==================================================
01-Dec-2019 07:44:55 downloaded 1.0 MB
01-Dec-2019 07:44:55
01-Dec-2019 07:44:55 * installing *source* package 'jsonlite' ...
01-Dec-2019 07:44:55 ** package 'jsonlite' successfully unpacked and MD5 sums checked
01-Dec-2019 07:44:55 ** libs
01-Dec-2019 07:44:55 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
01-Dec-2019 07:44:55 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
01-Dec-2019 07:44:55 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:56 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:57 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
01-Dec-2019 07:44:58 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
01-Dec-2019 07:44:58 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
01-Dec-2019 07:44:58 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
01-Dec-2019 07:44:58 installing to /usr/local/lib/R/site-library/jsonlite/libs
01-Dec-2019 07:44:58 ** R
01-Dec-2019 07:44:58 ** inst
01-Dec-2019 07:44:58 ** preparing package for lazy loading
01-Dec-2019 07:44:58 ** help
01-Dec-2019 07:44:58 *** installing help indices
01-Dec-2019 07:44:58 ** building package indices
01-Dec-2019 07:44:58 ** installing vignettes
01-Dec-2019 07:44:58 ** testing if installed package can be loaded
01-Dec-2019 07:44:58 * DONE (jsonlite)
01-Dec-2019 07:44:58
01-Dec-2019 07:44:58 The downloaded source packages are in
01-Dec-2019 07:44:58         '/tmp/RtmpciQJC5/downloaded_packages'
01-Dec-2019 07:44:58 [1] "/usr/local/lib/R/site-library/jsonlite"
01-Dec-2019 07:45:06 Removing intermediate container be19944ebf3c
01-Dec-2019 07:45:06 ---> fc3fe06d852c
01-Dec-2019 07:45:06 Step 5/11 : COPY r_extractor.py launcher.R /home/clowder/
01-Dec-2019 07:45:06 ---> 3de14977c939
01-Dec-2019 07:45:06 Step 6/11 : ONBUILD COPY packages.* Dockerfile /home/clowder/
01-Dec-2019 07:45:06 ---> Running in bcdc7e387552
01-Dec-2019 07:45:07 Removing intermediate container bcdc7e387552
01-Dec-2019 07:45:07 ---> 1c324cd235b1
01-Dec-2019 07:45:07 Step 7/11 : 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
01-Dec-2019 07:45:07 ---> Running in 274128062bf0
01-Dec-2019 07:45:07 Removing intermediate container 274128062bf0
01-Dec-2019 07:45:07 ---> b052c5a00deb
01-Dec-2019 07:45:07 Step 8/11 : ONBUILD COPY docker.R* Dockerfile /home/clowder/
01-Dec-2019 07:45:07 ---> Running in 1644120674d3
01-Dec-2019 07:45:08 Removing intermediate container 1644120674d3
01-Dec-2019 07:45:08 ---> c566eee0f099
01-Dec-2019 07:45:08 Step 9/11 : ONBUILD RUN if [ -e docker.R ]; then                 Rscript docker.R;             fi
01-Dec-2019 07:45:08 ---> Running in 318ab3d89bb5
01-Dec-2019 07:45:09 Removing intermediate container 318ab3d89bb5
01-Dec-2019 07:45:09 ---> ed28db4e0503
01-Dec-2019 07:45:09 Step 10/11 : ONBUILD ADD . /home/clowder/
01-Dec-2019 07:45:09 ---> Running in 499e06920c6b
01-Dec-2019 07:45:09 Removing intermediate container 499e06920c6b
01-Dec-2019 07:45:09 ---> 10da96b1af2d
01-Dec-2019 07:45:09 Step 11/11 : CMD python r_extractor.py
01-Dec-2019 07:45:09 ---> Running in 0416827b7713
01-Dec-2019 07:45:10 Removing intermediate container 0416827b7713
01-Dec-2019 07:45:10 ---> 40b7441754cc
01-Dec-2019 07:45:10 Successfully built 40b7441754cc
01-Dec-2019 07:45:10 Successfully tagged clowder/extractors-simple-r-extractor-python3:onbuild
01-Dec-2019 07:45:10 Sending build context to Docker daemon  9.216kB
01-Dec-2019 07:45:10
01-Dec-2019 07:45:10 Step 1/3 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:45:10 Step 2/3 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:onbuild
01-Dec-2019 07:45:10 # Executing 5 build triggers
01-Dec-2019 07:45:10 ---> Running in fb4d7021d168
01-Dec-2019 07:45:12 Removing intermediate container fb4d7021d168
01-Dec-2019 07:45:12 ---> Running in e3686e395451
01-Dec-2019 07:45:14 Removing intermediate container e3686e395451
01-Dec-2019 07:45:15 ---> 1da0549fb38e
01-Dec-2019 07:45:15 Step 3/3 : ENV MAIN_SCRIPT="wordcount.py"
01-Dec-2019 07:45:15 ---> Running in 0e91598f18f6
01-Dec-2019 07:45:15 Removing intermediate container 0e91598f18f6
01-Dec-2019 07:45:15 ---> 712594098076
01-Dec-2019 07:45:15 Successfully built 712594098076
01-Dec-2019 07:45:15 Successfully tagged clowder/extractors-wordcount:latest
01-Dec-2019 07:45:15 Sending build context to Docker daemon   5.12kB
01-Dec-2019 07:45:15
01-Dec-2019 07:45:15 Step 1/4 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:45:15 Step 2/4 : FROM clowder/extractors-simple-extractor${PYCLOWDER_PYTHON}:onbuild
01-Dec-2019 07:45:15 # Executing 5 build triggers
01-Dec-2019 07:45:16 ---> Running in 8f3ee5a857be
01-Dec-2019 07:45:18 Removing intermediate container 8f3ee5a857be
01-Dec-2019 07:45:19 ---> Running in fbe7cc2ff769
01-Dec-2019 07:45:20 Removing intermediate container fbe7cc2ff769
01-Dec-2019 07:45:21 ---> e6eedd360d46
01-Dec-2019 07:45:21 Step 3/4 : ENV EXTRACTION_FUNC="wordcount"
01-Dec-2019 07:45:21 ---> Running in 9f43d486c50a
01-Dec-2019 07:45:21 Removing intermediate container 9f43d486c50a
01-Dec-2019 07:45:21 ---> b9688e1e5d84
01-Dec-2019 07:45:21 Step 4/4 : ENV EXTRACTION_MODULE="wordcount"
01-Dec-2019 07:45:21 ---> Running in 98711b5c8f65
01-Dec-2019 07:45:22 Removing intermediate container 98711b5c8f65
01-Dec-2019 07:45:22 ---> 24d6064fc5f0
01-Dec-2019 07:45:22 Successfully built 24d6064fc5f0
01-Dec-2019 07:45:22 Successfully tagged clowder/extractors-wordcount-simple-extractor:latest
01-Dec-2019 07:45:22 Sending build context to Docker daemon   5.12kB
01-Dec-2019 07:45:22
01-Dec-2019 07:45:22 Step 1/3 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:45:22 Step 2/3 : FROM clowder/extractors-simple-r-extractor${PYCLOWDER_PYTHON}:onbuild
01-Dec-2019 07:45:22 # Executing 5 build triggers
01-Dec-2019 07:45:23 ---> Running in cb0ba471ebe2
01-Dec-2019 07:45:24 Removing intermediate container cb0ba471ebe2
01-Dec-2019 07:45:25 ---> Running in eea84ddb72fb
01-Dec-2019 07:45:27 Removing intermediate container eea84ddb72fb
01-Dec-2019 07:45:27 ---> c7094a27ff8d
01-Dec-2019 07:45:27 Step 3/3 : ENV R_SCRIPT="wordcount.R"     R_FUNCTION="process_file"
01-Dec-2019 07:45:27 ---> Running in d517cc0c953d
01-Dec-2019 07:45:27 Removing intermediate container d517cc0c953d
01-Dec-2019 07:45:27 ---> 3f1f7b7334de
01-Dec-2019 07:45:27 Successfully built 3f1f7b7334de
01-Dec-2019 07:45:27 Successfully tagged clowder/extractors-wordcount-simple-r-extractor:latest
01-Dec-2019 07:45:27 Sending build context to Docker daemon  8.192kB
01-Dec-2019 07:45:27
01-Dec-2019 07:45:28 Step 1/7 : FROM python:3.5
01-Dec-2019 07:45:28 3.5: Pulling from library/python
01-Dec-2019 07:45:28 16ea0e8c8879: Pulling fs layer
01-Dec-2019 07:45:28 50024b0106d5: Pulling fs layer
01-Dec-2019 07:45:28 ff95660c6937: Pulling fs layer
01-Dec-2019 07:45:28 9c7d0e5c0bc2: Pulling fs layer
01-Dec-2019 07:45:28 29c4fb388fdf: Pulling fs layer
01-Dec-2019 07:45:28 49a8841b38a3: Pulling fs layer
01-Dec-2019 07:45:28 a0a6062c45f4: Pulling fs layer
01-Dec-2019 07:45:28 314102e5cfb7: Pulling fs layer
01-Dec-2019 07:45:28 b84da28b0e51: Pulling fs layer
01-Dec-2019 07:45:28 49a8841b38a3: Waiting
01-Dec-2019 07:45:28 314102e5cfb7: Waiting
01-Dec-2019 07:45:28 9c7d0e5c0bc2: Waiting
01-Dec-2019 07:45:28 29c4fb388fdf: Waiting
01-Dec-2019 07:45:28 a0a6062c45f4: Waiting
01-Dec-2019 07:45:28 b84da28b0e51: Waiting
01-Dec-2019 07:45:29 50024b0106d5: Verifying Checksum
01-Dec-2019 07:45:29 50024b0106d5: Download complete
01-Dec-2019 07:45:29 ff95660c6937: Verifying Checksum
01-Dec-2019 07:45:29 ff95660c6937: Download complete
01-Dec-2019 07:45:30 16ea0e8c8879: Verifying Checksum
01-Dec-2019 07:45:30 16ea0e8c8879: Download complete
01-Dec-2019 07:45:30 49a8841b38a3: Verifying Checksum
01-Dec-2019 07:45:30 49a8841b38a3: Download complete
01-Dec-2019 07:45:30 9c7d0e5c0bc2: Verifying Checksum
01-Dec-2019 07:45:30 9c7d0e5c0bc2: Download complete
01-Dec-2019 07:45:30 314102e5cfb7: Verifying Checksum
01-Dec-2019 07:45:30 314102e5cfb7: Download complete
01-Dec-2019 07:45:31 b84da28b0e51: Verifying Checksum
01-Dec-2019 07:45:31 b84da28b0e51: Download complete
01-Dec-2019 07:45:31 a0a6062c45f4: Verifying Checksum
01-Dec-2019 07:45:31 a0a6062c45f4: Download complete
01-Dec-2019 07:45:33 16ea0e8c8879: Pull complete
01-Dec-2019 07:45:34 50024b0106d5: Pull complete
01-Dec-2019 07:45:35 29c4fb388fdf: Verifying Checksum
01-Dec-2019 07:45:35 29c4fb388fdf: Download complete
01-Dec-2019 07:45:40 ff95660c6937: Pull complete
01-Dec-2019 07:45:42 9c7d0e5c0bc2: Pull complete
01-Dec-2019 07:45:50 29c4fb388fdf: Pull complete
01-Dec-2019 07:45:51 49a8841b38a3: Pull complete
01-Dec-2019 07:45:55 a0a6062c45f4: Pull complete
01-Dec-2019 07:45:57 314102e5cfb7: Pull complete
01-Dec-2019 07:45:58 b84da28b0e51: Pull complete
01-Dec-2019 07:45:58 Digest: sha256:e7fb3ab522e4e6e9ffe78b30086c15025f53650c6d693e72d1f1b9e2e68b40e4
01-Dec-2019 07:45:58 Status: Downloaded newer image for python:3.5
01-Dec-2019 07:45:58 ---> 5be81bc3f1e6
01-Dec-2019 07:45:58 Step 2/7 : ENV RABBITMQ_URI="amqp://guest:guest@rabbitmq/%2F"
01-Dec-2019 07:45:59 ---> Running in 879f2e691a12
01-Dec-2019 07:45:59 Removing intermediate container 879f2e691a12
01-Dec-2019 07:45:59 ---> 776d9bc25f0f
01-Dec-2019 07:45:59 Step 3/7 : EXPOSE 9999
01-Dec-2019 07:45:59 ---> Running in cf6edcb0766b
01-Dec-2019 07:46:00 Removing intermediate container cf6edcb0766b
01-Dec-2019 07:46:00 ---> 3dd4e3666905
01-Dec-2019 07:46:00 Step 4/7 : RUN pip install pika==0.11.2 requests==2.18.4
01-Dec-2019 07:46:00 ---> Running in 0ee35855d6be
01-Dec-2019 07:46:02 Collecting pika==0.11.2
01-Dec-2019 07:46:02   Downloading https://files.pythonhosted.org/packages/76/b4/0ada6918ac79ce4d8d45d0ba436ee21a1ef685047fb1dde4d2de0178b327/pika-0.11.2-py2.py3-none-any.whl (107kB)
01-Dec-2019 07:46:02 Collecting requests==2.18.4
01-Dec-2019 07:46:02   Downloading https://files.pythonhosted.org/packages/49/df/50aa1999ab9bde74656c2919d9c0c085fd2b3775fd3eca826012bef76d8c/requests-2.18.4-py2.py3-none-any.whl (88kB)
01-Dec-2019 07:46:02 Collecting idna<2.7,>=2.5
01-Dec-2019 07:46:02   Downloading https://files.pythonhosted.org/packages/27/cc/6dd9a3869f15c2edfab863b992838277279ce92663d334df9ecf5106f5c6/idna-2.6-py2.py3-none-any.whl (56kB)
01-Dec-2019 07:46:02 Collecting certifi>=2017.4.17
01-Dec-2019 07:46:02   Downloading https://files.pythonhosted.org/packages/b9/63/df50cac98ea0d5b006c55a399c3bf1db9da7b5a24de7890bc9cfd5dd9e99/certifi-2019.11.28-py2.py3-none-any.whl (156kB)
01-Dec-2019 07:46:03 Collecting urllib3<1.23,>=1.21.1
01-Dec-2019 07:46:03   Downloading https://files.pythonhosted.org/packages/63/cb/6965947c13a94236f6d4b8223e21beb4d576dc72e8130bd7880f600839b8/urllib3-1.22-py2.py3-none-any.whl (132kB)
01-Dec-2019 07:46:03 Collecting chardet<3.1.0,>=3.0.2
01-Dec-2019 07:46:03   Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)
01-Dec-2019 07:46:03 Installing collected packages: pika, idna, certifi, urllib3, chardet, requests
01-Dec-2019 07:46:03 Successfully installed certifi-2019.11.28 chardet-3.0.4 idna-2.6 pika-0.11.2 requests-2.18.4 urllib3-1.22
01-Dec-2019 07:46:05 Removing intermediate container 0ee35855d6be
01-Dec-2019 07:46:05 ---> 553785aaf315
01-Dec-2019 07:46:05 Step 5/7 : WORKDIR /src
01-Dec-2019 07:46:05 ---> Running in 7ad623629e3f
01-Dec-2019 07:46:05 Removing intermediate container 7ad623629e3f
01-Dec-2019 07:46:05 ---> a12d43591beb
01-Dec-2019 07:46:05 Step 6/7 : COPY monitor.py /src/
01-Dec-2019 07:46:06 ---> 9107ae1a6ce9
01-Dec-2019 07:46:06 Step 7/7 : CMD python monitor.py
01-Dec-2019 07:46:06 ---> Running in ee5920980335
01-Dec-2019 07:46:06 Removing intermediate container ee5920980335
01-Dec-2019 07:46:06 ---> f12ad9a235b0
01-Dec-2019 07:46:06 Successfully built f12ad9a235b0
01-Dec-2019 07:46:06 Successfully tagged clowder/extractors-monitor:latest
01-Dec-2019 07:46:06 Finished task 'docker build' with result: Success
01-Dec-2019 07:46:06 Starting task 'docker push' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
01-Dec-2019 07:46:06
Beginning to execute external process for build 'Clowder - pyclowder2 - docker-build-upgrade-pip - Default Job #1 (CATS-PYC2105-JOB1-1)'
... running command line:
/bin/sh release.sh
... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC2105-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=docker-build-upgrade-pip
bamboo_capability_system_builder_command_npm_6=/home/bamboo/node-v6.9.1/bin/npm
bamboo_capability_system_builder_command_buckminster_4_3=/home/bamboo/buckminster-4.3/buckminster
bamboo_capability_system_builder_node_Node_js_v6_9_1=/home/bamboo/node-v6.9.1/bin/node
bamboo_capability_system_builder_command_buckminster_4_4=/home/bamboo/buckminster-4.4/buckminster
bamboo_capability_system_builder_command_buckminster_4_2=/home/bamboo/buckminster-4.2/buckminster
bamboo_planRepository_1_branchDisplayName=docker-build-upgrade-pip
bamboo_repository_revision_number=ef55c798a38049d1889c3283adaf7fa63ca180ae
bamboo_resultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PYC2105-JOB1-1
bamboo_capability_system_builder_command_sphinx=/usr/bin/sphinx-build
bamboo_build_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC2105-JOB1
bamboo_planRepository_1_name=pyclowder2
bamboo_buildKey=CATS-PYC2105-JOB1
bamboo_capability_system_os=linux
bamboo_shortPlanName=pyclowder2
bamboo_planRepository_name=pyclowder2
bamboo_buildNumber=1
bamboo_capability_system_builder_node_grunt_6=/home/bamboo/node-v6.9.1/bin/grunt
bamboo_shortJobName=Default Job
bamboo_capability_system_builder_command_python3_6=/usr/bin/python3.6
bamboo_buildResultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-PYC2105-JOB1-1
bamboo_planRepository_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder2.git
bamboo_agentId=143032321
bamboo_planName=Clowder - pyclowder2 - docker-build-upgrade-pip
bamboo_repository_179109891_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder2.git
bamboo_build_commandline_com_atlassian_bamboo_plugins_scripttask_task_builder_script_6=/home/bamboo/bamboo-agent-home/temp/CATS-PYC2105-JOB1-1-ScriptBuildTask-2520226215210995388.sh
bamboo_shortPlanKey=PYC2105
bamboo_capability_system_builder_command_sbt_0_13=/home/bamboo/sbt-0.13.2/bin/sbt
bamboo_capability_system_builder_node_Node_js_v0_10_28=/home/bamboo/node-v0.10.28/bin/node
bamboo_shortJobKey=JOB1
bamboo_planRepository_revision=ef55c798a38049d1889c3283adaf7fa63ca180ae
bamboo_buildTimeStamp=2019-12-01T07:34:44.998-06:00
bamboo_capability_system_builder_command_npm=/home/bamboo/node-v0.10.28/bin/npm
bamboo_capability_system_builder_mvn2_Maven_2=/home/bamboo/apache-maven-2.2.1
bamboo_build_commandline_com_atlassian_bamboo_plugins_scripttask_task_builder_script_3=/home/bamboo/bamboo-agent-home/temp/CATS-PYC2105-JOB1-1-ScriptBuildTask-2284821256874184438.sh
bamboo_repository_179109891_git_username=
bamboo_build_commandline_com_atlassian_bamboo_plugins_scripttask_task_builder_script_2=/bin/sh docker.sh
bamboo_repository_git_branch=docker-build-upgrade-pip
bamboo_buildResultKey=CATS-PYC2105-JOB1-1
bamboo_repository_branch_name=docker-build-upgrade-pip
bamboo_buildPlanName=Clowder - pyclowder2 - docker-build-upgrade-pip - Default Job
bamboo_planRepository_1_revision=ef55c798a38049d1889c3283adaf7fa63ca180ae
bamboo_capability_system_builder_command_python3=/usr/bin/python3
bamboo_repository_name=pyclowder2
bamboo_buildFailed=false
bamboo_capability_system_docker_executable=/usr/bin/docker
bamboo_capability_system_builder_command_grunt=/home/bamboo/node-v0.10.28/bin/grunt
bamboo_repository_179109891_branch_name=docker-build-upgrade-pip
bamboo_planRepository_branch=docker-build-upgrade-pip
bamboo_agentWorkingDirectory=/home/bamboo/bamboo-agent-home/xml-data/build-dir
bamboo_capability_system_git_executable=/usr/bin/git
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bamboo_capability_system_builder_sbt_SBT_0_13_13=/home/bamboo/sbt-0.13.13
bamboo_planRepository_branchDisplayName=docker-build-upgrade-pip
bamboo_capability_system_builder_command_phantomjs=/home/bamboo/phantomjs-1.9.8/bin/phantomjs
bamboo_planRepository_1_type=bbserver
bamboo_planRepository_branchName=docker-build-upgrade-pip
bamboo_capability_system_builder_command_python2_7=/usr/bin/python2.7
bamboo_capability_system_hostname=buildserver-1
bamboo_capability_system_jdk_JDK=/home/bamboo/jdk1.8.0_66
bamboo_capability_system_software_mongo=/usr/bin/mongo
bamboo_plan_storageTag=plan-178978819
bamboo_hg_cache_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/_hg-repositories-cache
bamboo_capability_system_builder_command_casperjs=/home/bamboo/node-v0.10.28/bin/casperjs
bamboo_capability_system_software_rabbitmq=/usr/sbin/rabbitmqctl
bamboo_capability_system_jdk_JDK_1_8_0_66=/home/bamboo/jdk1.8.0_66
bamboo_planRepository_1_username=
bamboo_planRepository_type=bbserver
bamboo_repository_179109891_revision_number=ef55c798a38049d1889c3283adaf7fa63ca180ae
bamboo_git_cache_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/_git-repositories-cache
bamboo_repository_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder2.git
bamboo_capability_system_builder_node_Node_js=/home/bamboo/node-v0.10.28/bin/node
bamboo_capability_system_builder_node_Node_js_v9_3_0=/home/bamboo/node-v9.3.0/bin/node
bamboo_capability_system_builder_ant_Ant=/home/bamboo/apache-ant-1.9.4
bamboo_capability_system_builder_mvn3_Maven_3=/home/bamboo/apache-maven-3.3.9
bamboo_tmp_directory=/home/bamboo/bamboo-agent-home/temp
bamboo_repository_179109891_git_branch=docker-build-upgrade-pip
bamboo_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC2105-JOB1
bamboo_planKey=CATS-PYC2105
bamboo_planRepository_1_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/pyclowder2.git
bamboo_planRepository_username=
bamboo_capability_system_jdk_JDK_1_8=/home/bamboo/jdk1.8.0_66
bamboo_capability_system_jdk_JDK_1_6=/home/bamboo/jdk1.6.0_41
bamboo_capability_system_builder_command_mkcrx=/home/bamboo/mkcrx/mkcrx.sh
bamboo_capability_system_jdk_JDK_1_7=/home/bamboo/jdk1.7.0_60
bamboo_planRepository_1_branchName=docker-build-upgrade-pip
bamboo_repository_179109891_name=pyclowder2
01-Dec-2019 07:46:06 Sending build context to Docker daemon  284.7kB
01-Dec-2019 07:46:06
01-Dec-2019 07:46:06 Step 1/10 : FROM ubuntu:16.04
01-Dec-2019 07:46:06 ---> 56bab49eef2e
01-Dec-2019 07:46:06 Step 2/10 : ARG PYTHON_VERSION="2.7"
01-Dec-2019 07:46:06 ---> Using cache
01-Dec-2019 07:46:06 ---> 93e46200d603
01-Dec-2019 07:46:06 Step 3/10 : ENV PYTHON_VERSION=${PYTHON_VERSION}     RABBITMQ_URI="amqp://guest:guest@rabbitmq:5672/%2F"     RABBITMQ_EXCHANGE="clowder"     RABBITMQ_QUEUE=""     REGISTRATION_ENDPOINTS=""     EMAIL_SERVER=""     EMAIL_SENDER="extractor"     MAIN_SCRIPT=""
01-Dec-2019 07:46:06 ---> Using cache
01-Dec-2019 07:46:06 ---> e24243e39985
01-Dec-2019 07:46:06 Step 4/10 : RUN apt-get -q -q update     && apt-get install -y --no-install-recommends python${PYTHON_VERSION} curl     && if [ ! -e /usr/bin/python ]; then ln -s /usr/bin/python${PYTHON_VERSION} /usr/bin/python; fi     && curl -k https://bootstrap.pypa.io/get-pip.py -o /tmp/get-pip.py     && python /tmp/get-pip.py     && pip install --upgrade setuptools     && pip install --upgrade pip     && rm -rf /var/lib/apt/lists/* /tmp/get-pip.py
01-Dec-2019 07:46:06 ---> Using cache
01-Dec-2019 07:46:06 ---> a16f8db5df3c
01-Dec-2019 07:46:06 Step 5/10 : COPY pyclowder /tmp/pyclowder/pyclowder
01-Dec-2019 07:46:06 ---> Using cache
01-Dec-2019 07:46:06 ---> 06caffd64802
01-Dec-2019 07:46:06 Step 6/10 : COPY setup.py description.rst /tmp/pyclowder/
01-Dec-2019 07:46:06 ---> Using cache
01-Dec-2019 07:46:06 ---> 24e7aa1f6ef0
01-Dec-2019 07:46:06 Step 7/10 : RUN pip install --upgrade /tmp/pyclowder     && rm -rf /tmp/pyclowder
01-Dec-2019 07:46:06 ---> Using cache
01-Dec-2019 07:46:06 ---> b76d2b81879a
01-Dec-2019 07:46:06 Step 8/10 : WORKDIR /home/clowder
01-Dec-2019 07:46:06 ---> Using cache
01-Dec-2019 07:46:06 ---> a52d3c87a8fd
01-Dec-2019 07:46:06 Step 9/10 : COPY notifications.json /home/clowder/
01-Dec-2019 07:46:06 ---> Using cache
01-Dec-2019 07:46:06 ---> 3a8d882b39e6
01-Dec-2019 07:46:06 Step 10/10 : CMD python "./${MAIN_SCRIPT}"
01-Dec-2019 07:46:06 ---> Using cache
01-Dec-2019 07:46:06 ---> 4f0abdafa099
01-Dec-2019 07:46:06 Successfully built 4f0abdafa099
01-Dec-2019 07:46:07 Successfully tagged clowder/pyclowder:latest
01-Dec-2019 07:46:07 Sending build context to Docker daemon  282.6kB
01-Dec-2019 07:46:07
01-Dec-2019 07:46:07 Step 1/7 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:07 Step 2/7 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest
01-Dec-2019 07:46:07 ---> 4f0abdafa099
01-Dec-2019 07:46:07 Step 3/7 : ONBUILD COPY packages.* Dockerfile /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> b8b59ed02b34
01-Dec-2019 07:46:07 Step 4/7 : 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
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 307bc92590a2
01-Dec-2019 07:46:07 Step 5/7 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 70bc834459e2
01-Dec-2019 07:46:07 Step 6/7 : ONBUILD RUN if [ -e requirements.txt ]; then                 pip install --no-cache-dir -r requirements.txt;             fi
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> d715b7b081cd
01-Dec-2019 07:46:07 Step 7/7 : ONBUILD ADD . /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> ce03cb4962f1
01-Dec-2019 07:46:07 Successfully built ce03cb4962f1
01-Dec-2019 07:46:07 Successfully tagged clowder/pyclowder:onbuild
01-Dec-2019 07:46:07 Sending build context to Docker daemon   12.8kB
01-Dec-2019 07:46:07
01-Dec-2019 07:46:07 Step 1/6 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:07 Step 2/6 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:onbuild
01-Dec-2019 07:46:07 # Executing 5 build triggers
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 82fa242b6b52
01-Dec-2019 07:46:07 Step 3/6 : ENV MAIN_SCRIPT="binary_extractor.py"     RABBITMQ_QUEUE=""     IMAGE_BINARY=""     IMAGE_TYPE=""     IMAGE_THUMBNAIL_COMMAND=""     IMAGE_PREVIEW_COMMAND=""     PREVIEW_BINARY=""     PREVIEW_TYPE=""     PREVIEW_COMMAND=""
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 6eaafe3f472c
01-Dec-2019 07:46:07 Step 4/6 : ONBUILD COPY packages.* Dockerfile /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> f31c18cd2a5c
01-Dec-2019 07:46:07 Step 5/6 : ONBUILD RUN if [ -e packages.apt ]; then                 apt-get -q -q update                 && xargs apt-get -y install --no-install-recommends < packages.apt                 && rm -rf /var/lib/apt/lists/*;             fi
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 7892c997afe0
01-Dec-2019 07:46:07 Step 6/6 : ONBUILD COPY extractor_info.json /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 4b61c130122b
01-Dec-2019 07:46:07 Successfully built 4b61c130122b
01-Dec-2019 07:46:07 Successfully tagged clowder/extractors-binary-preview:onbuild
01-Dec-2019 07:46:07 Sending build context to Docker daemon  6.656kB
01-Dec-2019 07:46:07
01-Dec-2019 07:46:07 Step 1/11 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:07 Step 2/11 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest
01-Dec-2019 07:46:07 ---> 4f0abdafa099
01-Dec-2019 07:46:07 Step 3/11 : ENV EXTRACTION_FUNC=""
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 2f87d66875a5
01-Dec-2019 07:46:07 Step 4/11 : ENV EXTRACTION_MODULE=""
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 14a3fac6b001
01-Dec-2019 07:46:07 Step 5/11 : COPY simple_extractor.py .
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 0116b67027e8
01-Dec-2019 07:46:07 Step 6/11 : ONBUILD COPY packages.* Dockerfile /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 599660aaf264
01-Dec-2019 07:46:07 Step 7/11 : 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
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 3cbd78e64d8c
01-Dec-2019 07:46:07 Step 8/11 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> c598cc816b80
01-Dec-2019 07:46:07 Step 9/11 : ONBUILD RUN if [ -e requirements.txt ]; then                 pip install --no-cache-dir -r requirements.txt;             fi
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 259981581bd8
01-Dec-2019 07:46:07 Step 10/11 : ONBUILD ADD . /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 626e88dc83c4
01-Dec-2019 07:46:07 Step 11/11 : CMD python -c "from simple_extractor import SimplePythonExtractor; from ${EXTRACTION_MODULE} import *; SimplePythonExtractor(${EXTRACTION_FUNC}).start()"
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 8007029907fd
01-Dec-2019 07:46:07 Successfully built 8007029907fd
01-Dec-2019 07:46:07 Successfully tagged clowder/extractors-simple-extractor:onbuild
01-Dec-2019 07:46:07 Sending build context to Docker daemon  13.31kB
01-Dec-2019 07:46:07
01-Dec-2019 07:46:07 Step 1/11 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:07 Step 2/11 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest
01-Dec-2019 07:46:07 ---> 4f0abdafa099
01-Dec-2019 07:46:07 Step 3/11 : ENV R_SCRIPT=""     R_FUNCTION=""
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> fc8d4e715461
01-Dec-2019 07:46:07 Step 4/11 : 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-keys E298A3A825C0D65DFD57CBB651716619E084DAB9     && 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') == ''))"
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 6e9e078ecdb3
01-Dec-2019 07:46:07 Step 5/11 : COPY r_extractor.py launcher.R /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 0f44ff51f1db
01-Dec-2019 07:46:07 Step 6/11 : ONBUILD COPY packages.* Dockerfile /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> a310bd0290b9
01-Dec-2019 07:46:07 Step 7/11 : 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
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 1eafc3025a08
01-Dec-2019 07:46:07 Step 8/11 : ONBUILD COPY docker.R* Dockerfile /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> b987f6301c9b
01-Dec-2019 07:46:07 Step 9/11 : ONBUILD RUN if [ -e docker.R ]; then                 Rscript docker.R;             fi
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 39c2940bdf36
01-Dec-2019 07:46:07 Step 10/11 : ONBUILD ADD . /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 8137d9a52bcb
01-Dec-2019 07:46:07 Step 11/11 : CMD python r_extractor.py
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 24503eaa7a0a
01-Dec-2019 07:46:07 Successfully built 24503eaa7a0a
01-Dec-2019 07:46:07 Successfully tagged clowder/extractors-simple-r-extractor:onbuild
01-Dec-2019 07:46:07 Sending build context to Docker daemon  284.7kB
01-Dec-2019 07:46:07
01-Dec-2019 07:46:07 Step 1/10 : FROM ubuntu:16.04
01-Dec-2019 07:46:07 ---> 56bab49eef2e
01-Dec-2019 07:46:07 Step 2/10 : ARG PYTHON_VERSION="2.7"
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 93e46200d603
01-Dec-2019 07:46:07 Step 3/10 : ENV PYTHON_VERSION=${PYTHON_VERSION}     RABBITMQ_URI="amqp://guest:guest@rabbitmq:5672/%2F"     RABBITMQ_EXCHANGE="clowder"     RABBITMQ_QUEUE=""     REGISTRATION_ENDPOINTS=""     EMAIL_SERVER=""     EMAIL_SENDER="extractor"     MAIN_SCRIPT=""
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 6f4761625f1e
01-Dec-2019 07:46:07 Step 4/10 : RUN apt-get -q -q update     && apt-get install -y --no-install-recommends python${PYTHON_VERSION} curl     && if [ ! -e /usr/bin/python ]; then ln -s /usr/bin/python${PYTHON_VERSION} /usr/bin/python; fi     && curl -k https://bootstrap.pypa.io/get-pip.py -o /tmp/get-pip.py     && python /tmp/get-pip.py     && pip install --upgrade setuptools     && pip install --upgrade pip     && rm -rf /var/lib/apt/lists/* /tmp/get-pip.py
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> a79d45a2a5fd
01-Dec-2019 07:46:07 Step 5/10 : COPY pyclowder /tmp/pyclowder/pyclowder
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 63fdc1cf5ef3
01-Dec-2019 07:46:07 Step 6/10 : COPY setup.py description.rst /tmp/pyclowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 33740b8edb6f
01-Dec-2019 07:46:07 Step 7/10 : RUN pip install --upgrade /tmp/pyclowder     && rm -rf /tmp/pyclowder
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 6d0824da3340
01-Dec-2019 07:46:07 Step 8/10 : WORKDIR /home/clowder
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> aeed12fffa49
01-Dec-2019 07:46:07 Step 9/10 : COPY notifications.json /home/clowder/
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> c4700a8f68bb
01-Dec-2019 07:46:07 Step 10/10 : CMD python "./${MAIN_SCRIPT}"
01-Dec-2019 07:46:07 ---> Using cache
01-Dec-2019 07:46:07 ---> 7006ab85b609
01-Dec-2019 07:46:07 Successfully built 7006ab85b609
01-Dec-2019 07:46:07 Successfully tagged clowder/pyclowder-python3:latest
01-Dec-2019 07:46:08 Sending build context to Docker daemon  282.6kB
01-Dec-2019 07:46:08
01-Dec-2019 07:46:08 Step 1/7 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:08 Step 2/7 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest
01-Dec-2019 07:46:08 ---> 7006ab85b609
01-Dec-2019 07:46:08 Step 3/7 : ONBUILD COPY packages.* Dockerfile /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 6d1ff63ad7f2
01-Dec-2019 07:46:08 Step 4/7 : 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
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 4211289d207f
01-Dec-2019 07:46:08 Step 5/7 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> df9915138fe9
01-Dec-2019 07:46:08 Step 6/7 : ONBUILD RUN if [ -e requirements.txt ]; then                 pip install --no-cache-dir -r requirements.txt;             fi
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 3d7388f05ee3
01-Dec-2019 07:46:08 Step 7/7 : ONBUILD ADD . /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> ed8e9de7f486
01-Dec-2019 07:46:08 Successfully built ed8e9de7f486
01-Dec-2019 07:46:08 Successfully tagged clowder/pyclowder-python3:onbuild
01-Dec-2019 07:46:08 Sending build context to Docker daemon   12.8kB
01-Dec-2019 07:46:08
01-Dec-2019 07:46:08 Step 1/6 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:08 Step 2/6 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:onbuild
01-Dec-2019 07:46:08 # Executing 5 build triggers
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> bc01e117a869
01-Dec-2019 07:46:08 Step 3/6 : ENV MAIN_SCRIPT="binary_extractor.py"     RABBITMQ_QUEUE=""     IMAGE_BINARY=""     IMAGE_TYPE=""     IMAGE_THUMBNAIL_COMMAND=""     IMAGE_PREVIEW_COMMAND=""     PREVIEW_BINARY=""     PREVIEW_TYPE=""     PREVIEW_COMMAND=""
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 992499553391
01-Dec-2019 07:46:08 Step 4/6 : ONBUILD COPY packages.* Dockerfile /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 13aa1b8178fc
01-Dec-2019 07:46:08 Step 5/6 : ONBUILD RUN if [ -e packages.apt ]; then                 apt-get -q -q update                 && xargs apt-get -y install --no-install-recommends < packages.apt                 && rm -rf /var/lib/apt/lists/*;             fi
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 8db34a4a8272
01-Dec-2019 07:46:08 Step 6/6 : ONBUILD COPY extractor_info.json /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 1efaac141c12
01-Dec-2019 07:46:08 Successfully built 1efaac141c12
01-Dec-2019 07:46:08 Successfully tagged clowder/extractors-binary-preview-python3:onbuild
01-Dec-2019 07:46:08 Sending build context to Docker daemon  6.656kB
01-Dec-2019 07:46:08
01-Dec-2019 07:46:08 Step 1/11 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:08 Step 2/11 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest
01-Dec-2019 07:46:08 ---> 7006ab85b609
01-Dec-2019 07:46:08 Step 3/11 : ENV EXTRACTION_FUNC=""
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 298e09b12726
01-Dec-2019 07:46:08 Step 4/11 : ENV EXTRACTION_MODULE=""
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 00ac3d41d739
01-Dec-2019 07:46:08 Step 5/11 : COPY simple_extractor.py .
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> c93f8efe0cdb
01-Dec-2019 07:46:08 Step 6/11 : ONBUILD COPY packages.* Dockerfile /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 3a4f472ce8f5
01-Dec-2019 07:46:08 Step 7/11 : 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
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> cc75a114a3b3
01-Dec-2019 07:46:08 Step 8/11 : ONBUILD COPY requirements.txt* Dockerfile /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> dfe7c19f67fa
01-Dec-2019 07:46:08 Step 9/11 : ONBUILD RUN if [ -e requirements.txt ]; then                 pip install --no-cache-dir -r requirements.txt;             fi
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 626d85817eef
01-Dec-2019 07:46:08 Step 10/11 : ONBUILD ADD . /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> aab0463e9b56
01-Dec-2019 07:46:08 Step 11/11 : CMD python -c "from simple_extractor import SimplePythonExtractor; from ${EXTRACTION_MODULE} import *; SimplePythonExtractor(${EXTRACTION_FUNC}).start()"
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 03ae8a94c93c
01-Dec-2019 07:46:08 Successfully built 03ae8a94c93c
01-Dec-2019 07:46:08 Successfully tagged clowder/extractors-simple-extractor-python3:onbuild
01-Dec-2019 07:46:08 Sending build context to Docker daemon  13.31kB
01-Dec-2019 07:46:08
01-Dec-2019 07:46:08 Step 1/11 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:08 Step 2/11 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:latest
01-Dec-2019 07:46:08 ---> 7006ab85b609
01-Dec-2019 07:46:08 Step 3/11 : ENV R_SCRIPT=""     R_FUNCTION=""
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> a7e8d647e7f8
01-Dec-2019 07:46:08 Step 4/11 : 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-keys E298A3A825C0D65DFD57CBB651716619E084DAB9     && 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') == ''))"
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> fc3fe06d852c
01-Dec-2019 07:46:08 Step 5/11 : COPY r_extractor.py launcher.R /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 3de14977c939
01-Dec-2019 07:46:08 Step 6/11 : ONBUILD COPY packages.* Dockerfile /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 1c324cd235b1
01-Dec-2019 07:46:08 Step 7/11 : 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
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> b052c5a00deb
01-Dec-2019 07:46:08 Step 8/11 : ONBUILD COPY docker.R* Dockerfile /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> c566eee0f099
01-Dec-2019 07:46:08 Step 9/11 : ONBUILD RUN if [ -e docker.R ]; then                 Rscript docker.R;             fi
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> ed28db4e0503
01-Dec-2019 07:46:08 Step 10/11 : ONBUILD ADD . /home/clowder/
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 10da96b1af2d
01-Dec-2019 07:46:08 Step 11/11 : CMD python r_extractor.py
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 40b7441754cc
01-Dec-2019 07:46:08 Successfully built 40b7441754cc
01-Dec-2019 07:46:08 Successfully tagged clowder/extractors-simple-r-extractor-python3:onbuild
01-Dec-2019 07:46:08 Sending build context to Docker daemon  9.216kB
01-Dec-2019 07:46:08
01-Dec-2019 07:46:08 Step 1/3 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:08 Step 2/3 : FROM clowder/pyclowder${PYCLOWDER_PYTHON}:onbuild
01-Dec-2019 07:46:08 # Executing 5 build triggers
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 1da0549fb38e
01-Dec-2019 07:46:08 Step 3/3 : ENV MAIN_SCRIPT="wordcount.py"
01-Dec-2019 07:46:08 ---> Using cache
01-Dec-2019 07:46:08 ---> 712594098076
01-Dec-2019 07:46:08 Successfully built 712594098076
01-Dec-2019 07:46:08 Successfully tagged clowder/extractors-wordcount:latest
01-Dec-2019 07:46:08 Sending build context to Docker daemon   5.12kB
01-Dec-2019 07:46:08
01-Dec-2019 07:46:09 Step 1/4 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:09 Step 2/4 : FROM clowder/extractors-simple-extractor${PYCLOWDER_PYTHON}:onbuild
01-Dec-2019 07:46:09 # Executing 5 build triggers
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> e6eedd360d46
01-Dec-2019 07:46:09 Step 3/4 : ENV EXTRACTION_FUNC="wordcount"
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> b9688e1e5d84
01-Dec-2019 07:46:09 Step 4/4 : ENV EXTRACTION_MODULE="wordcount"
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> 24d6064fc5f0
01-Dec-2019 07:46:09 Successfully built 24d6064fc5f0
01-Dec-2019 07:46:09 Successfully tagged clowder/extractors-wordcount-simple-extractor:latest
01-Dec-2019 07:46:09 Sending build context to Docker daemon   5.12kB
01-Dec-2019 07:46:09
01-Dec-2019 07:46:09 Step 1/3 : ARG PYCLOWDER_PYTHON=""
01-Dec-2019 07:46:09 Step 2/3 : FROM clowder/extractors-simple-r-extractor${PYCLOWDER_PYTHON}:onbuild
01-Dec-2019 07:46:09 # Executing 5 build triggers
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> c7094a27ff8d
01-Dec-2019 07:46:09 Step 3/3 : ENV R_SCRIPT="wordcount.R"     R_FUNCTION="process_file"
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> 3f1f7b7334de
01-Dec-2019 07:46:09 Successfully built 3f1f7b7334de
01-Dec-2019 07:46:09 Successfully tagged clowder/extractors-wordcount-simple-r-extractor:latest
01-Dec-2019 07:46:09 Sending build context to Docker daemon  8.192kB
01-Dec-2019 07:46:09
01-Dec-2019 07:46:09 Step 1/7 : FROM python:3.5
01-Dec-2019 07:46:09 ---> 5be81bc3f1e6
01-Dec-2019 07:46:09 Step 2/7 : ENV RABBITMQ_URI="amqp://guest:guest@rabbitmq/%2F"
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> 776d9bc25f0f
01-Dec-2019 07:46:09 Step 3/7 : EXPOSE 9999
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> 3dd4e3666905
01-Dec-2019 07:46:09 Step 4/7 : RUN pip install pika==0.11.2 requests==2.18.4
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> 553785aaf315
01-Dec-2019 07:46:09 Step 5/7 : WORKDIR /src
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> a12d43591beb
01-Dec-2019 07:46:09 Step 6/7 : COPY monitor.py /src/
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> 9107ae1a6ce9
01-Dec-2019 07:46:09 Step 7/7 : CMD python monitor.py
01-Dec-2019 07:46:09 ---> Using cache
01-Dec-2019 07:46:09 ---> f12ad9a235b0
01-Dec-2019 07:46:09 Successfully built f12ad9a235b0
01-Dec-2019 07:46:09 Successfully tagged clowder/extractors-monitor:latest
01-Dec-2019 07:46:09 Finished task 'docker push' with result: Success
01-Dec-2019 07:46:09 Starting task 'test results' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.junit'
01-Dec-2019 07:46:09 Parsing test results under /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-PYC2105-JOB1...
01-Dec-2019 07:46:09 Finished task 'test results' with result: Success
01-Dec-2019 07:46:09 Running post build plugin 'Docker Container Cleanup'
01-Dec-2019 07:46:09 Running post build plugin 'NCover Results Collector'
01-Dec-2019 07:46:09 Running post build plugin 'Clover Results Collector'
01-Dec-2019 07:46:09 Running post build plugin 'npm Cache Cleanup'
01-Dec-2019 07:46:09 Running post build plugin 'Artifact Copier'
01-Dec-2019 07:46:09 Finalising the build...
01-Dec-2019 07:46:09 Stopping timer.
01-Dec-2019 07:46:09 Build CATS-PYC2105-JOB1-1 completed.
01-Dec-2019 07:46:09 Running on server: post build plugin 'NCover Results Collector'
01-Dec-2019 07:46:09 Running on server: post build plugin 'Build Hanging Detection Configuration'
01-Dec-2019 07:46:09 Running on server: post build plugin 'Clover Delta Calculator'
01-Dec-2019 07:46:09 Running on server: post build plugin 'Maven Dependencies Postprocessor'
01-Dec-2019 07:46:09 All post build plugins have finished
01-Dec-2019 07:46:09 Generating build results summary...
01-Dec-2019 07:46:09 Saving build results to disk...
01-Dec-2019 07:46:10 Logging substituted variables...
01-Dec-2019 07:46:10 Indexing build results...
01-Dec-2019 07:46:10 Finished building CATS-PYC2105-JOB1-1.