Build: #40 was successful
Job: Default Job was successful
Build log
The build generated 1,062 lines of output. The output is too long and has been truncated to the last 1,000 lines. Download or view full build log.
| 17-Aug-2019 20:19:22 | libxext6 libxmu6 libxt6 wget x11-common |
| 17-Aug-2019 20:19:22 | 0 upgraded, 13 newly installed, 0 to remove and 55 not upgraded. |
| 17-Aug-2019 20:19:22 | Need to get 1402 kB of archives. |
| 17-Aug-2019 20:19:22 | After this operation, 5597 kB of additional disk space will be used. |
| 17-Aug-2019 20:19:22 | Get:1 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B] |
| 17-Aug-2019 20:19:22 | Get:2 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [11.0 kB] |
| 17-Aug-2019 20:19:22 | Get:3 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxcb1 amd64 1.11.1-1ubuntu1 [40.0 kB] |
| 17-Aug-2019 20:19:22 | Get:4 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libx11-data all 2:1.6.3-1ubuntu2.1 [113 kB] |
| 17-Aug-2019 20:19:22 | Get:5 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libx11-6 amd64 2:1.6.3-1ubuntu2.1 [570 kB] |
| 17-Aug-2019 20:19:23 | Get:6 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB] |
| 17-Aug-2019 20:19:23 | Get:7 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 x11-common all 1:7.7+13ubuntu3.1 [22.9 kB] |
| 17-Aug-2019 20:19:23 | Get:8 http://archive.ubuntu.com/ubuntu xenial/main amd64 libice6 amd64 2:1.0.9-1 [39.2 kB] |
| 17-Aug-2019 20:19:23 | Get:9 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB] |
| 17-Aug-2019 20:19:23 | Get:10 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libidn11 amd64 1.32-3ubuntu1.2 [46.5 kB] |
| 17-Aug-2019 20:19:23 | Get:11 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 wget amd64 1.17.1-1ubuntu1.5 [299 kB] |
| 17-Aug-2019 20:19:23 | Get:12 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxt6 amd64 1:1.1.5-0ubuntu1 [160 kB] |
| 17-Aug-2019 20:19:23 | Get:13 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxmu6 amd64 2:1.1.2-2 [46.0 kB] |
| 17-Aug-2019 20:19:23 | debconf: delaying package configuration, since apt-utils is not installed |
| 17-Aug-2019 20:19:23 | Fetched 1402 kB in 0s (1612 kB/s) |
| 17-Aug-2019 20:19:24 | Selecting previously unselected package libxau6:amd64. |
| 17-Aug-2019 20:19:24 | (Reading database ... |
| 17-Aug-2019 20:19:24 | (Reading database ... 5% |
| 17-Aug-2019 20:19:24 | (Reading database ... 10% |
| 17-Aug-2019 20:19:24 | (Reading database ... 15% |
| 17-Aug-2019 20:19:24 | (Reading database ... 20% |
| 17-Aug-2019 20:19:24 | (Reading database ... 25% |
| 17-Aug-2019 20:19:24 | (Reading database ... 30% |
| 17-Aug-2019 20:19:24 | (Reading database ... 35% |
| 17-Aug-2019 20:19:24 | (Reading database ... 40% |
| 17-Aug-2019 20:19:24 | (Reading database ... 45% |
| 17-Aug-2019 20:19:24 | (Reading database ... 50% |
| 17-Aug-2019 20:19:24 | (Reading database ... 55% |
| 17-Aug-2019 20:19:24 | (Reading database ... 60% |
| 17-Aug-2019 20:19:24 | (Reading database ... 65% |
| 17-Aug-2019 20:19:24 | (Reading database ... 70% |
| 17-Aug-2019 20:19:24 | (Reading database ... 75% |
| 17-Aug-2019 20:19:24 | (Reading database ... 80% |
| 17-Aug-2019 20:19:24 | (Reading database ... 85% |
| 17-Aug-2019 20:19:24 | (Reading database ... 90% |
| 17-Aug-2019 20:19:24 | (Reading database ... 95% |
| 17-Aug-2019 20:19:24 | (Reading database ... 100% |
| 17-Aug-2019 20:19:24 | (Reading database ... 6101 files and directories currently installed.) |
| 17-Aug-2019 20:19:24 | Preparing to unpack .../libxau6_1%3a1.0.8-1_amd64.deb ... |
| 17-Aug-2019 20:19:24 | Unpacking libxau6:amd64 (1:1.0.8-1) ... |
| 17-Aug-2019 20:19:24 | Selecting previously unselected package libxdmcp6:amd64. |
| 17-Aug-2019 20:19:24 | Preparing to unpack .../libxdmcp6_1%3a1.1.2-1.1_amd64.deb ... |
| 17-Aug-2019 20:19:24 | Unpacking libxdmcp6:amd64 (1:1.1.2-1.1) ... |
| 17-Aug-2019 20:19:25 | Selecting previously unselected package libxcb1:amd64. |
| 17-Aug-2019 20:19:25 | Preparing to unpack .../libxcb1_1.11.1-1ubuntu1_amd64.deb ... |
| 17-Aug-2019 20:19:25 | Unpacking libxcb1:amd64 (1.11.1-1ubuntu1) ... |
| 17-Aug-2019 20:19:25 | Selecting previously unselected package libx11-data. |
| 17-Aug-2019 20:19:25 | Preparing to unpack .../libx11-data_2%3a1.6.3-1ubuntu2.1_all.deb ... |
| 17-Aug-2019 20:19:25 | Unpacking libx11-data (2:1.6.3-1ubuntu2.1) ... |
| 17-Aug-2019 20:19:27 | Selecting previously unselected package libx11-6:amd64. |
| 17-Aug-2019 20:19:27 | Preparing to unpack .../libx11-6_2%3a1.6.3-1ubuntu2.1_amd64.deb ... |
| 17-Aug-2019 20:19:27 | Unpacking libx11-6:amd64 (2:1.6.3-1ubuntu2.1) ... |
| 17-Aug-2019 20:19:28 | Selecting previously unselected package libxext6:amd64. |
| 17-Aug-2019 20:19:28 | Preparing to unpack .../libxext6_2%3a1.3.3-1_amd64.deb ... |
| 17-Aug-2019 20:19:29 | Unpacking libxext6:amd64 (2:1.3.3-1) ... |
| 17-Aug-2019 20:19:29 | Selecting previously unselected package x11-common. |
| 17-Aug-2019 20:19:29 | Preparing to unpack .../x11-common_1%3a7.7+13ubuntu3.1_all.deb ... |
| 17-Aug-2019 20:19:29 | dpkg-query: no packages found matching nux-tools |
| 17-Aug-2019 20:19:29 | Unpacking x11-common (1:7.7+13ubuntu3.1) ... |
| 17-Aug-2019 20:19:30 | Selecting previously unselected package libice6:amd64. |
| 17-Aug-2019 20:19:30 | Preparing to unpack .../libice6_2%3a1.0.9-1_amd64.deb ... |
| 17-Aug-2019 20:19:30 | Unpacking libice6:amd64 (2:1.0.9-1) ... |
| 17-Aug-2019 20:19:32 | Selecting previously unselected package libsm6:amd64. |
| 17-Aug-2019 20:19:32 | Preparing to unpack .../libsm6_2%3a1.2.2-1_amd64.deb ... |
| 17-Aug-2019 20:19:32 | Unpacking libsm6:amd64 (2:1.2.2-1) ... |
| 17-Aug-2019 20:19:33 | Selecting previously unselected package libidn11:amd64. |
| 17-Aug-2019 20:19:33 | Preparing to unpack .../libidn11_1.32-3ubuntu1.2_amd64.deb ... |
| 17-Aug-2019 20:19:33 | Unpacking libidn11:amd64 (1.32-3ubuntu1.2) ... |
| 17-Aug-2019 20:19:34 | Selecting previously unselected package wget. |
| 17-Aug-2019 20:19:34 | Preparing to unpack .../wget_1.17.1-1ubuntu1.5_amd64.deb ... |
| 17-Aug-2019 20:19:34 | Unpacking wget (1.17.1-1ubuntu1.5) ... |
| 17-Aug-2019 20:19:35 | Selecting previously unselected package libxt6:amd64. |
| 17-Aug-2019 20:19:35 | Preparing to unpack .../libxt6_1%3a1.1.5-0ubuntu1_amd64.deb ... |
| 17-Aug-2019 20:19:35 | Unpacking libxt6:amd64 (1:1.1.5-0ubuntu1) ... |
| 17-Aug-2019 20:19:36 | Selecting previously unselected package libxmu6:amd64. |
| 17-Aug-2019 20:19:36 | Preparing to unpack .../libxmu6_2%3a1.1.2-2_amd64.deb ... |
| 17-Aug-2019 20:19:36 | Unpacking libxmu6:amd64 (2:1.1.2-2) ... |
| 17-Aug-2019 20:19:37 | Processing triggers for libc-bin (2.23-0ubuntu9) ... |
| 17-Aug-2019 20:19:37 | Processing triggers for systemd (229-4ubuntu19) ... |
| 17-Aug-2019 20:19:37 | Setting up libxau6:amd64 (1:1.0.8-1) ... |
| 17-Aug-2019 20:19:38 | Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ... |
| 17-Aug-2019 20:19:38 | Setting up libxcb1:amd64 (1.11.1-1ubuntu1) ... |
| 17-Aug-2019 20:19:39 | Setting up libx11-data (2:1.6.3-1ubuntu2.1) ... |
| 17-Aug-2019 20:19:39 | Setting up libx11-6:amd64 (2:1.6.3-1ubuntu2.1) ... |
| 17-Aug-2019 20:19:40 | Setting up libxext6:amd64 (2:1.3.3-1) ... |
| 17-Aug-2019 20:19:40 | Setting up x11-common (1:7.7+13ubuntu3.1) ... |
| 17-Aug-2019 20:19:42 | debconf: unable to initialize frontend: Dialog |
| 17-Aug-2019 20:19:42 | debconf: (TERM is not set, so the dialog frontend is not usable.) |
| 17-Aug-2019 20:19:42 | debconf: falling back to frontend: Readline |
| 17-Aug-2019 20:19:42 | debconf: unable to initialize frontend: Readline |
| 17-Aug-2019 20:19:42 | 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.) |
| 17-Aug-2019 20:19:42 | debconf: falling back to frontend: Teletype |
| 17-Aug-2019 20:19:42 | update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults |
| 17-Aug-2019 20:19:42 | invoke-rc.d: could not determine current runlevel |
| 17-Aug-2019 20:19:42 | invoke-rc.d: policy-rc.d denied execution of start. |
| 17-Aug-2019 20:19:42 | Setting up libice6:amd64 (2:1.0.9-1) ... |
| 17-Aug-2019 20:19:43 | Setting up libsm6:amd64 (2:1.2.2-1) ... |
| 17-Aug-2019 20:19:44 | Setting up libidn11:amd64 (1.32-3ubuntu1.2) ... |
| 17-Aug-2019 20:19:44 | Setting up wget (1.17.1-1ubuntu1.5) ... |
| 17-Aug-2019 20:19:44 | Setting up libxt6:amd64 (1:1.1.5-0ubuntu1) ... |
| 17-Aug-2019 20:19:44 | Setting up libxmu6:amd64 (2:1.1.2-2) ... |
| 17-Aug-2019 20:19:45 | Processing triggers for libc-bin (2.23-0ubuntu9) ... |
| 17-Aug-2019 20:19:45 | Processing triggers for systemd (229-4ubuntu19) ... |
| 17-Aug-2019 20:19:47 | Removing intermediate container 77f6ff928732 |
| 17-Aug-2019 20:19:47 | ---> 2c019d780774 |
| 17-Aug-2019 20:19:47 | Step 8/11 : USER clowder |
| 17-Aug-2019 20:19:48 | ---> Running in b825a8e5fee0 |
| 17-Aug-2019 20:19:49 | Removing intermediate container b825a8e5fee0 |
| 17-Aug-2019 20:19:49 | ---> ce435c4e674d |
| 17-Aug-2019 20:19:49 | Step 9/11 : COPY entrypoint.sh *.py *.m data/*.mat *.json /home/clowder/ |
| 17-Aug-2019 20:19:51 | ---> 10aeaabd067e |
| 17-Aug-2019 20:19:51 | Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"] |
| 17-Aug-2019 20:19:51 | ---> Running in f0aaea24b033 |
| 17-Aug-2019 20:19:51 | Removing intermediate container f0aaea24b033 |
| 17-Aug-2019 20:19:51 | ---> 3144db607c40 |
| 17-Aug-2019 20:19:51 | Step 11/11 : CMD ["extractor"] |
| 17-Aug-2019 20:19:52 | ---> Running in 242cab7d6529 |
| 17-Aug-2019 20:19:53 | Removing intermediate container 242cab7d6529 |
| 17-Aug-2019 20:19:53 | ---> 121042f8ed7e |
| 17-Aug-2019 20:19:53 | Successfully built 121042f8ed7e |
| 17-Aug-2019 20:19:53 | Successfully tagged 5903:latest |
| 17-Aug-2019 20:19:54 | The push refers to repository [docker.io/clowder/extractors-msc-kidney] |
| 17-Aug-2019 20:19:54 | af84e69b700c: Preparing |
| 17-Aug-2019 20:19:54 | 18c165cdf8c8: Preparing |
| 17-Aug-2019 20:19:54 | ee18a427d82a: Preparing |
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| 17-Aug-2019 20:19:54 | a2022691bf95: Preparing |
| 17-Aug-2019 20:19:54 | 59669fcdd5eb: Waiting |
| 17-Aug-2019 20:19:54 | 7f7a065d245a: Waiting |
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| 17-Aug-2019 20:19:54 | c56153825175: Waiting |
| 17-Aug-2019 20:19:54 | ae620432889d: Waiting |
| 17-Aug-2019 20:19:54 | a2022691bf95: Waiting |
| 17-Aug-2019 20:19:54 | 0fbe2bcb1bf9: Waiting |
| 17-Aug-2019 20:19:54 | f2297bdfc824: Layer already exists |
| 17-Aug-2019 20:19:54 | 0cdb02ac1d86: Layer already exists |
| 17-Aug-2019 20:19:55 | 0fbe2bcb1bf9: Layer already exists |
| 17-Aug-2019 20:19:55 | 59669fcdd5eb: Layer already exists |
| 17-Aug-2019 20:19:55 | 7f7a065d245a: Layer already exists |
| 17-Aug-2019 20:19:55 | f96e6b25195f: Layer already exists |
| 17-Aug-2019 20:19:55 | c56153825175: Layer already exists |
| 17-Aug-2019 20:19:55 | ae620432889d: Layer already exists |
| 17-Aug-2019 20:19:55 | a2022691bf95: Layer already exists |
| 17-Aug-2019 20:19:56 | af84e69b700c: Pushed |
| 17-Aug-2019 20:19:56 | 18c165cdf8c8: Pushed |
| 17-Aug-2019 20:19:56 | ee18a427d82a: Pushed |
| 17-Aug-2019 20:19:59 | browndog_v0.2.0: digest: sha256:84a6605aaf1c5c36f8305aab20360aed8b0ff6a349dbbf7365ca9294f1827f47 size: 2826 |
| 17-Aug-2019 20:19:59 | The push refers to repository [docker.io/clowder/extractors-msc-kidney] |
| 17-Aug-2019 20:19:59 | af84e69b700c: Preparing |
| 17-Aug-2019 20:19:59 | 18c165cdf8c8: Preparing |
| 17-Aug-2019 20:19:59 | ee18a427d82a: Preparing |
| 17-Aug-2019 20:19:59 | 0cdb02ac1d86: Preparing |
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| 17-Aug-2019 20:19:59 | a2022691bf95: Preparing |
| 17-Aug-2019 20:19:59 | 0fbe2bcb1bf9: Waiting |
| 17-Aug-2019 20:19:59 | c56153825175: Waiting |
| 17-Aug-2019 20:19:59 | ae620432889d: Waiting |
| 17-Aug-2019 20:19:59 | 59669fcdd5eb: Waiting |
| 17-Aug-2019 20:19:59 | a2022691bf95: Waiting |
| 17-Aug-2019 20:19:59 | 7f7a065d245a: Waiting |
| 17-Aug-2019 20:19:59 | f96e6b25195f: Waiting |
| 17-Aug-2019 20:20:00 | f2297bdfc824: Layer already exists |
| 17-Aug-2019 20:20:00 | ee18a427d82a: Layer already exists |
| 17-Aug-2019 20:20:00 | 0cdb02ac1d86: Layer already exists |
| 17-Aug-2019 20:20:00 | af84e69b700c: Layer already exists |
| 17-Aug-2019 20:20:00 | 18c165cdf8c8: Layer already exists |
| 17-Aug-2019 20:20:00 | 0fbe2bcb1bf9: Layer already exists |
| 17-Aug-2019 20:20:00 | f96e6b25195f: Layer already exists |
| 17-Aug-2019 20:20:00 | 59669fcdd5eb: Layer already exists |
| 17-Aug-2019 20:20:00 | c56153825175: Layer already exists |
| 17-Aug-2019 20:20:00 | 7f7a065d245a: Layer already exists |
| 17-Aug-2019 20:20:00 | ae620432889d: Layer already exists |
| 17-Aug-2019 20:20:00 | a2022691bf95: Layer already exists |
| 17-Aug-2019 20:20:01 | browndog_v0.3.0: digest: sha256:84a6605aaf1c5c36f8305aab20360aed8b0ff6a349dbbf7365ca9294f1827f47 size: 2826 |
| 17-Aug-2019 20:20:01 | The push refers to repository [docker.io/clowder/extractors-msc-kidney] |
| 17-Aug-2019 20:20:01 | af84e69b700c: Preparing |
| 17-Aug-2019 20:20:01 | 18c165cdf8c8: Preparing |
| 17-Aug-2019 20:20:01 | ee18a427d82a: Preparing |
| 17-Aug-2019 20:20:01 | 0cdb02ac1d86: Preparing |
| 17-Aug-2019 20:20:01 | f2297bdfc824: Preparing |
| 17-Aug-2019 20:20:01 | 0fbe2bcb1bf9: Preparing |
| 17-Aug-2019 20:20:01 | 59669fcdd5eb: Preparing |
| 17-Aug-2019 20:20:01 | 7f7a065d245a: Preparing |
| 17-Aug-2019 20:20:01 | f96e6b25195f: Preparing |
| 17-Aug-2019 20:20:01 | c56153825175: Preparing |
| 17-Aug-2019 20:20:01 | ae620432889d: Preparing |
| 17-Aug-2019 20:20:01 | a2022691bf95: Preparing |
| 17-Aug-2019 20:20:01 | 59669fcdd5eb: Waiting |
| 17-Aug-2019 20:20:01 | 7f7a065d245a: Waiting |
| 17-Aug-2019 20:20:01 | f96e6b25195f: Waiting |
| 17-Aug-2019 20:20:01 | c56153825175: Waiting |
| 17-Aug-2019 20:20:01 | 0fbe2bcb1bf9: Waiting |
| 17-Aug-2019 20:20:01 | ae620432889d: Waiting |
| 17-Aug-2019 20:20:01 | a2022691bf95: Waiting |
| 17-Aug-2019 20:20:01 | 18c165cdf8c8: Layer already exists |
| 17-Aug-2019 20:20:02 | 0cdb02ac1d86: Layer already exists |
| 17-Aug-2019 20:20:02 | ee18a427d82a: Layer already exists |
| 17-Aug-2019 20:20:02 | af84e69b700c: Layer already exists |
| 17-Aug-2019 20:20:02 | f2297bdfc824: Layer already exists |
| 17-Aug-2019 20:20:02 | 7f7a065d245a: Layer already exists |
| 17-Aug-2019 20:20:02 | 0fbe2bcb1bf9: Layer already exists |
| 17-Aug-2019 20:20:02 | c56153825175: Layer already exists |
| 17-Aug-2019 20:20:02 | ae620432889d: Layer already exists |
| 17-Aug-2019 20:20:02 | 59669fcdd5eb: Layer already exists |
| 17-Aug-2019 20:20:02 | f96e6b25195f: Layer already exists |
| 17-Aug-2019 20:20:02 | a2022691bf95: Layer already exists |
| 17-Aug-2019 20:20:03 | latest: digest: sha256:84a6605aaf1c5c36f8305aab20360aed8b0ff6a349dbbf7365ca9294f1827f47 size: 2826 |
| 17-Aug-2019 20:20:03 | Untagged: 5903:latest |
| 17-Aug-2019 20:20:03 | Sending build context to Docker daemon 67.07kB |
| 17-Aug-2019 20:20:03 | |
| 17-Aug-2019 20:20:03 | Step 1/11 : FROM clowder/pyclowder:1 |
| 17-Aug-2019 20:20:03 | ---> d1a9e970ed30 |
| 17-Aug-2019 20:20:03 | Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu> |
| 17-Aug-2019 20:20:04 | ---> Running in 2642227af74e |
| 17-Aug-2019 20:20:04 | Removing intermediate container 2642227af74e |
| 17-Aug-2019 20:20:04 | ---> 46f6d1fdf076 |
| 17-Aug-2019 20:20:04 | Step 3/11 : ENV RABBITMQ_URI="" RABBITMQ_EXCHANGE="clowder" RABBITMQ_VHOST="%2F" RABBITMQ_QUEUE="ncsa.msc.IsletExtractor" MONGO_URI="" DB_USERNAME="" DB_PASSWORD="" MAIN_SCRIPT="extractor-Islet.py" |
| 17-Aug-2019 20:20:04 | ---> Running in 5c7c383af8e0 |
| 17-Aug-2019 20:20:05 | Removing intermediate container 5c7c383af8e0 |
| 17-Aug-2019 20:20:05 | ---> af9d0d799b73 |
| 17-Aug-2019 20:20:05 | Step 4/11 : USER root |
| 17-Aug-2019 20:20:05 | ---> Running in e6e7075b7730 |
| 17-Aug-2019 20:20:06 | Removing intermediate container e6e7075b7730 |
| 17-Aug-2019 20:20:06 | ---> 23fdccd890ec |
| 17-Aug-2019 20:20:06 | Step 5/11 : COPY requirements.txt /home/clowder/ |
| 17-Aug-2019 20:20:07 | ---> 3b2ac778ff8b |
| 17-Aug-2019 20:20:07 | Step 6/11 : RUN pip install --upgrade pip |
| 17-Aug-2019 20:20:07 | ---> Running in f4d97ba420ee |
| 17-Aug-2019 20:20:09 | Collecting pip |
| 17-Aug-2019 20:20:09 | Downloading https://files.pythonhosted.org/packages/8d/07/f7d7ced2f97ca3098c16565efbe6b15fafcba53e8d9bdb431e09140514b0/pip-19.2.2-py2.py3-none-any.whl (1.4MB) |
| 17-Aug-2019 20:20:09 | Installing collected packages: pip |
| 17-Aug-2019 20:20:09 | Found existing installation: pip 8.1.1 |
| 17-Aug-2019 20:20:09 | Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr |
| 17-Aug-2019 20:20:10 | Successfully installed pip-19.2.2 |
| 17-Aug-2019 20:20:12 | Removing intermediate container f4d97ba420ee |
| 17-Aug-2019 20:20:12 | ---> 61fe9668549b |
| 17-Aug-2019 20:20:12 | Step 7/11 : RUN pip install -r /home/clowder/requirements.txt |
| 17-Aug-2019 20:20:12 | ---> Running in 5c99558a171f |
| 17-Aug-2019 20:20:15 | DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support |
| 17-Aug-2019 20:20:15 | Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) (1.2.1) |
| 17-Aug-2019 20:20:15 | Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2)) |
| 17-Aug-2019 20:20:15 | Downloading https://files.pythonhosted.org/packages/96/53/3782b6cc03500c0949a7ba9dba0c70da95d63d0ed4a04446123987ff983f/openpyxl-1.6.2.tar.gz (199kB) |
| 17-Aug-2019 20:20:15 | Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3)) |
| 17-Aug-2019 20:20:15 | Downloading https://files.pythonhosted.org/packages/2b/5b/4c5b6eafc63e0985b926267579a1e2534af70df0a45932f0c23fcc5f1b88/pika-0.9.14.tar.gz (72kB) |
| 17-Aug-2019 20:20:15 | Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4)) |
| 17-Aug-2019 20:20:16 | Downloading https://files.pythonhosted.org/packages/d7/94/9aa9ddd3e885caa307c0db8af5a1f5d266d3db44e1ae89bd4e14841ab8d0/pymongo-3.2.1.tar.gz (647kB) |
| 17-Aug-2019 20:20:16 | Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5)) |
| 17-Aug-2019 20:20:17 | Downloading https://files.pythonhosted.org/packages/e2/8d/af599c0388f46775c6b039d8b9c4acda2f6ef86787312a35291fff4cb7ca/pytz-2014.3.tar.bz2 (158kB) |
| 17-Aug-2019 20:20:17 | Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6)) |
| 17-Aug-2019 20:20:17 | Downloading https://files.pythonhosted.org/packages/7d/15/6efffc6aee666e1456852c2bf1d483b46bf971a2d509b35a98fc3eae1c60/requests-2.2.1-py2.py3-none-any.whl (625kB) |
| 17-Aug-2019 20:20:17 | Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) (0.1.2) |
| 17-Aug-2019 20:20:17 | Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8)) |
| 17-Aug-2019 20:20:17 | Downloading https://files.pythonhosted.org/packages/b1/13/6fbcb55fef0b34c70cb3753741eaafc0e91553a1318653587a7d145caf15/xlrd-0.9.3.tar.gz (178kB) |
| 17-Aug-2019 20:20:18 | Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd |
| 17-Aug-2019 20:20:18 | Running setup.py install for openpyxl: started |
| 17-Aug-2019 20:20:18 | Running setup.py install for openpyxl: finished with status 'done' |
| 17-Aug-2019 20:20:18 | Found existing installation: pika 0.11.0 |
| 17-Aug-2019 20:20:18 | Uninstalling pika-0.11.0: |
| 17-Aug-2019 20:20:18 | Successfully uninstalled pika-0.11.0 |
| 17-Aug-2019 20:20:18 | Running setup.py install for pika: started |
| 17-Aug-2019 20:20:18 | Running setup.py install for pika: finished with status 'done' |
| 17-Aug-2019 20:20:18 | Running setup.py install for pymongo: started |
| 17-Aug-2019 20:20:19 | Running setup.py install for pymongo: finished with status 'done' |
| 17-Aug-2019 20:20:19 | Running setup.py install for pytz: started |
| 17-Aug-2019 20:20:19 | Running setup.py install for pytz: finished with status 'done' |
| 17-Aug-2019 20:20:19 | Found existing installation: requests 2.18.4 |
| 17-Aug-2019 20:20:19 | Uninstalling requests-2.18.4: |
| 17-Aug-2019 20:20:19 | Successfully uninstalled requests-2.18.4 |
| 17-Aug-2019 20:20:19 | Running setup.py install for xlrd: started |
| 17-Aug-2019 20:20:20 | Running setup.py install for xlrd: finished with status 'done' |
| 17-Aug-2019 20:20:20 | Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3 |
| 17-Aug-2019 20:20:22 | Removing intermediate container 5c99558a171f |
| 17-Aug-2019 20:20:22 | ---> 0ca0af53c3d9 |
| 17-Aug-2019 20:20:22 | Step 8/11 : USER clowder |
| 17-Aug-2019 20:20:23 | ---> Running in 3dbdee021426 |
| 17-Aug-2019 20:20:23 | Removing intermediate container 3dbdee021426 |
| 17-Aug-2019 20:20:23 | ---> 616b5d3c750b |
| 17-Aug-2019 20:20:23 | Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/ |
| 17-Aug-2019 20:20:24 | ---> 6ddcfe283daf |
| 17-Aug-2019 20:20:24 | Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"] |
| 17-Aug-2019 20:20:24 | ---> Running in e145cf7a8c4b |
| 17-Aug-2019 20:20:25 | Removing intermediate container e145cf7a8c4b |
| 17-Aug-2019 20:20:25 | ---> f37d40b6aa68 |
| 17-Aug-2019 20:20:25 | Step 11/11 : CMD ["extractor"] |
| 17-Aug-2019 20:20:25 | ---> Running in d4e5e94afccf |
| 17-Aug-2019 20:20:26 | Removing intermediate container d4e5e94afccf |
| 17-Aug-2019 20:20:26 | ---> 85500ed90c5e |
| 17-Aug-2019 20:20:26 | Successfully built 85500ed90c5e |
| 17-Aug-2019 20:20:26 | Successfully tagged 5903:latest |
| 17-Aug-2019 20:20:26 | The push refers to repository [docker.io/clowder/extractors-msc-islet] |
| 17-Aug-2019 20:20:27 | dfd2181cf16e: Preparing |
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| 17-Aug-2019 20:20:27 | 0cdb02ac1d86: Layer already exists |
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| 17-Aug-2019 20:20:28 | dfd2181cf16e: Pushed |
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| 17-Aug-2019 20:20:28 | c56153825175: Layer already exists |
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| 17-Aug-2019 20:20:29 | 4f423416bc8b: Pushed |
| 17-Aug-2019 20:20:29 | 2baf610cb686: Pushed |
| 17-Aug-2019 20:20:31 | browndog_v0.2.0: digest: sha256:c90c27244fa5a60e1fbeb4fb4365c426df627e6257391abeac420cc384572367 size: 3031 |
| 17-Aug-2019 20:20:32 | The push refers to repository [docker.io/clowder/extractors-msc-islet] |
| 17-Aug-2019 20:20:32 | dfd2181cf16e: Preparing |
| 17-Aug-2019 20:20:32 | 2baf610cb686: Preparing |
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| 17-Aug-2019 20:20:32 | a2022691bf95: Preparing |
| 17-Aug-2019 20:20:32 | f2297bdfc824: Waiting |
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| 17-Aug-2019 20:20:32 | c56153825175: Waiting |
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| 17-Aug-2019 20:20:32 | fe60c3145332: Layer already exists |
| 17-Aug-2019 20:20:32 | 2baf610cb686: Layer already exists |
| 17-Aug-2019 20:20:32 | 4f423416bc8b: Layer already exists |
| 17-Aug-2019 20:20:32 | dfd2181cf16e: Layer already exists |
| 17-Aug-2019 20:20:32 | 0cdb02ac1d86: Layer already exists |
| 17-Aug-2019 20:20:32 | f2297bdfc824: Layer already exists |
| 17-Aug-2019 20:20:32 | 0fbe2bcb1bf9: Layer already exists |
| 17-Aug-2019 20:20:32 | 59669fcdd5eb: Layer already exists |
| 17-Aug-2019 20:20:32 | 7f7a065d245a: Layer already exists |
| 17-Aug-2019 20:20:33 | f96e6b25195f: Layer already exists |
| 17-Aug-2019 20:20:33 | c56153825175: Layer already exists |
| 17-Aug-2019 20:20:33 | ae620432889d: Layer already exists |
| 17-Aug-2019 20:20:33 | a2022691bf95: Layer already exists |
| 17-Aug-2019 20:20:33 | browndog_v0.3.0: digest: sha256:c90c27244fa5a60e1fbeb4fb4365c426df627e6257391abeac420cc384572367 size: 3031 |
| 17-Aug-2019 20:20:34 | The push refers to repository [docker.io/clowder/extractors-msc-islet] |
| 17-Aug-2019 20:20:34 | dfd2181cf16e: Preparing |
| 17-Aug-2019 20:20:34 | 2baf610cb686: Preparing |
| 17-Aug-2019 20:20:34 | 4f423416bc8b: Preparing |
| 17-Aug-2019 20:20:34 | fe60c3145332: Preparing |
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| 17-Aug-2019 20:20:34 | c56153825175: Preparing |
| 17-Aug-2019 20:20:34 | ae620432889d: Preparing |
| 17-Aug-2019 20:20:34 | a2022691bf95: Preparing |
| 17-Aug-2019 20:20:34 | f2297bdfc824: Waiting |
| 17-Aug-2019 20:20:34 | 0fbe2bcb1bf9: Waiting |
| 17-Aug-2019 20:20:34 | 59669fcdd5eb: Waiting |
| 17-Aug-2019 20:20:34 | 7f7a065d245a: Waiting |
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| 17-Aug-2019 20:20:34 | c56153825175: Waiting |
| 17-Aug-2019 20:20:34 | ae620432889d: Waiting |
| 17-Aug-2019 20:20:34 | a2022691bf95: Waiting |
| 17-Aug-2019 20:20:34 | 4f423416bc8b: Layer already exists |
| 17-Aug-2019 20:20:34 | 0cdb02ac1d86: Layer already exists |
| 17-Aug-2019 20:20:34 | dfd2181cf16e: Layer already exists |
| 17-Aug-2019 20:20:34 | fe60c3145332: Layer already exists |
| 17-Aug-2019 20:20:34 | 2baf610cb686: Layer already exists |
| 17-Aug-2019 20:20:34 | f2297bdfc824: Layer already exists |
| 17-Aug-2019 20:20:34 | 0fbe2bcb1bf9: Layer already exists |
| 17-Aug-2019 20:20:34 | 7f7a065d245a: Layer already exists |
| 17-Aug-2019 20:20:34 | 59669fcdd5eb: Layer already exists |
| 17-Aug-2019 20:20:34 | f96e6b25195f: Layer already exists |
| 17-Aug-2019 20:20:34 | c56153825175: Layer already exists |
| 17-Aug-2019 20:20:34 | a2022691bf95: Layer already exists |
| 17-Aug-2019 20:20:35 | ae620432889d: Layer already exists |
| 17-Aug-2019 20:20:35 | latest: digest: sha256:c90c27244fa5a60e1fbeb4fb4365c426df627e6257391abeac420cc384572367 size: 3031 |
| 17-Aug-2019 20:20:35 | Untagged: 5903:latest |
| 17-Aug-2019 20:20:35 | Sending build context to Docker daemon 66.05kB |
| 17-Aug-2019 20:20:35 | |
| 17-Aug-2019 20:20:35 | Step 1/11 : FROM clowder/pyclowder:1 |
| 17-Aug-2019 20:20:35 | ---> d1a9e970ed30 |
| 17-Aug-2019 20:20:35 | Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu> |
| 17-Aug-2019 20:20:35 | ---> Using cache |
| 17-Aug-2019 20:20:35 | ---> 46f6d1fdf076 |
| 17-Aug-2019 20:20:35 | Step 3/11 : ENV RABBITMQ_URI="" RABBITMQ_EXCHANGE="clowder" RABBITMQ_VHOST="%2F" RABBITMQ_QUEUE="ncsa.msc.ChemCBCExtractor" MONGO_URI="" DB_USERNAME="" DB_PASSWORD="" MAIN_SCRIPT="extractor-Chem.py" |
| 17-Aug-2019 20:20:36 | ---> Running in 768456e09d46 |
| 17-Aug-2019 20:20:36 | Removing intermediate container 768456e09d46 |
| 17-Aug-2019 20:20:36 | ---> 1ce841923ee8 |
| 17-Aug-2019 20:20:36 | Step 4/11 : USER root |
| 17-Aug-2019 20:20:36 | ---> Running in 3d4224514c81 |
| 17-Aug-2019 20:20:37 | Removing intermediate container 3d4224514c81 |
| 17-Aug-2019 20:20:37 | ---> 31f46bba6828 |
| 17-Aug-2019 20:20:37 | Step 5/11 : COPY requirements.txt /home/clowder/ |
| 17-Aug-2019 20:20:38 | ---> 56c4c259f8ba |
| 17-Aug-2019 20:20:38 | Step 6/11 : RUN pip install --upgrade pip |
| 17-Aug-2019 20:20:38 | ---> Running in b7686fc2e6a6 |
| 17-Aug-2019 20:20:40 | Collecting pip |
| 17-Aug-2019 20:20:40 | Downloading https://files.pythonhosted.org/packages/8d/07/f7d7ced2f97ca3098c16565efbe6b15fafcba53e8d9bdb431e09140514b0/pip-19.2.2-py2.py3-none-any.whl (1.4MB) |
| 17-Aug-2019 20:20:40 | Installing collected packages: pip |
| 17-Aug-2019 20:20:40 | Found existing installation: pip 8.1.1 |
| 17-Aug-2019 20:20:40 | Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr |
| 17-Aug-2019 20:20:41 | Successfully installed pip-19.2.2 |
| 17-Aug-2019 20:20:43 | Removing intermediate container b7686fc2e6a6 |
| 17-Aug-2019 20:20:43 | ---> ab0eaf595b56 |
| 17-Aug-2019 20:20:43 | Step 7/11 : RUN pip install -r /home/clowder/requirements.txt |
| 17-Aug-2019 20:20:43 | ---> Running in 4a948a80c4ed |
| 17-Aug-2019 20:20:44 | DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support |
| 17-Aug-2019 20:20:44 | Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) (1.2.1) |
| 17-Aug-2019 20:20:44 | Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2)) |
| 17-Aug-2019 20:20:45 | Downloading https://files.pythonhosted.org/packages/96/53/3782b6cc03500c0949a7ba9dba0c70da95d63d0ed4a04446123987ff983f/openpyxl-1.6.2.tar.gz (199kB) |
| 17-Aug-2019 20:20:45 | Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3)) |
| 17-Aug-2019 20:20:45 | Downloading https://files.pythonhosted.org/packages/2b/5b/4c5b6eafc63e0985b926267579a1e2534af70df0a45932f0c23fcc5f1b88/pika-0.9.14.tar.gz (72kB) |
| 17-Aug-2019 20:20:45 | Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4)) |
| 17-Aug-2019 20:20:46 | Downloading https://files.pythonhosted.org/packages/d7/94/9aa9ddd3e885caa307c0db8af5a1f5d266d3db44e1ae89bd4e14841ab8d0/pymongo-3.2.1.tar.gz (647kB) |
| 17-Aug-2019 20:20:46 | Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5)) |
| 17-Aug-2019 20:20:46 | Downloading https://files.pythonhosted.org/packages/e2/8d/af599c0388f46775c6b039d8b9c4acda2f6ef86787312a35291fff4cb7ca/pytz-2014.3.tar.bz2 (158kB) |
| 17-Aug-2019 20:20:47 | Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6)) |
| 17-Aug-2019 20:20:47 | Downloading https://files.pythonhosted.org/packages/7d/15/6efffc6aee666e1456852c2bf1d483b46bf971a2d509b35a98fc3eae1c60/requests-2.2.1-py2.py3-none-any.whl (625kB) |
| 17-Aug-2019 20:20:47 | Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) (0.1.2) |
| 17-Aug-2019 20:20:47 | Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8)) |
| 17-Aug-2019 20:20:47 | Downloading https://files.pythonhosted.org/packages/b1/13/6fbcb55fef0b34c70cb3753741eaafc0e91553a1318653587a7d145caf15/xlrd-0.9.3.tar.gz (178kB) |
| 17-Aug-2019 20:20:47 | Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd |
| 17-Aug-2019 20:20:47 | Running setup.py install for openpyxl: started |
| 17-Aug-2019 20:20:48 | Running setup.py install for openpyxl: finished with status 'done' |
| 17-Aug-2019 20:20:48 | Found existing installation: pika 0.11.0 |
| 17-Aug-2019 20:20:48 | Uninstalling pika-0.11.0: |
| 17-Aug-2019 20:20:48 | Successfully uninstalled pika-0.11.0 |
| 17-Aug-2019 20:20:48 | Running setup.py install for pika: started |
| 17-Aug-2019 20:20:48 | Running setup.py install for pika: finished with status 'done' |
| 17-Aug-2019 20:20:48 | Running setup.py install for pymongo: started |
| 17-Aug-2019 20:20:48 | Running setup.py install for pymongo: finished with status 'done' |
| 17-Aug-2019 20:20:48 | Running setup.py install for pytz: started |
| 17-Aug-2019 20:20:49 | Running setup.py install for pytz: finished with status 'done' |
| 17-Aug-2019 20:20:49 | Found existing installation: requests 2.18.4 |
| 17-Aug-2019 20:20:49 | Uninstalling requests-2.18.4: |
| 17-Aug-2019 20:20:49 | Successfully uninstalled requests-2.18.4 |
| 17-Aug-2019 20:20:49 | Running setup.py install for xlrd: started |
| 17-Aug-2019 20:20:50 | Running setup.py install for xlrd: finished with status 'done' |
| 17-Aug-2019 20:20:50 | Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3 |
| 17-Aug-2019 20:20:51 | Removing intermediate container 4a948a80c4ed |
| 17-Aug-2019 20:20:51 | ---> 8115d9f642e2 |
| 17-Aug-2019 20:20:51 | Step 8/11 : USER clowder |
| 17-Aug-2019 20:20:52 | ---> Running in 34ba97592dd2 |
| 17-Aug-2019 20:20:53 | Removing intermediate container 34ba97592dd2 |
| 17-Aug-2019 20:20:53 | ---> 64c03002ac37 |
| 17-Aug-2019 20:20:53 | Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/ |
| 17-Aug-2019 20:20:54 | ---> c483b1845260 |
| 17-Aug-2019 20:20:54 | Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"] |
| 17-Aug-2019 20:20:55 | ---> Running in c02a2923cbe2 |
| 17-Aug-2019 20:20:55 | Removing intermediate container c02a2923cbe2 |
| 17-Aug-2019 20:20:55 | ---> c15d5523124b |
| 17-Aug-2019 20:20:55 | Step 11/11 : CMD ["extractor"] |
| 17-Aug-2019 20:20:56 | ---> Running in 25ba79dc6873 |
| 17-Aug-2019 20:20:56 | Removing intermediate container 25ba79dc6873 |
| 17-Aug-2019 20:20:56 | ---> 5e9040bbdf15 |
| 17-Aug-2019 20:20:56 | Successfully built 5e9040bbdf15 |
| 17-Aug-2019 20:20:56 | Successfully tagged 5903:latest |
| 17-Aug-2019 20:20:56 | The push refers to repository [docker.io/clowder/extractors-msc-chemcbc] |
| 17-Aug-2019 20:20:57 | 1c090297c37c: Preparing |
| 17-Aug-2019 20:20:57 | 654c8e3bc7f1: Preparing |
| 17-Aug-2019 20:20:57 | 796d512eb240: Preparing |
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| 17-Aug-2019 20:21:02 | browndog_v0.2.0: digest: sha256:3c0f413530aae2c6974c55cc6b96ad409760a9055c41109d60ffc1910d440b53 size: 3031 |
| 17-Aug-2019 20:21:02 | The push refers to repository [docker.io/clowder/extractors-msc-chemcbc] |
| 17-Aug-2019 20:21:02 | 1c090297c37c: Preparing |
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| 17-Aug-2019 20:21:03 | browndog_v0.3.0: digest: sha256:3c0f413530aae2c6974c55cc6b96ad409760a9055c41109d60ffc1910d440b53 size: 3031 |
| 17-Aug-2019 20:21:04 | The push refers to repository [docker.io/clowder/extractors-msc-chemcbc] |
| 17-Aug-2019 20:21:04 | 1c090297c37c: Preparing |
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| 17-Aug-2019 20:21:04 | 796d512eb240: Layer already exists |
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| 17-Aug-2019 20:21:04 | ae620432889d: Layer already exists |
| 17-Aug-2019 20:21:05 | a2022691bf95: Layer already exists |
| 17-Aug-2019 20:21:05 | latest: digest: sha256:3c0f413530aae2c6974c55cc6b96ad409760a9055c41109d60ffc1910d440b53 size: 3031 |
| 17-Aug-2019 20:21:05 | Untagged: 5903:latest |
| 17-Aug-2019 20:21:05 | Sending build context to Docker daemon 198.1kB |
| 17-Aug-2019 20:21:05 | |
| 17-Aug-2019 20:21:05 | Step 1/11 : FROM clowder/pyclowder:1 |
| 17-Aug-2019 20:21:05 | ---> d1a9e970ed30 |
| 17-Aug-2019 20:21:05 | Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu> |
| 17-Aug-2019 20:21:05 | ---> Using cache |
| 17-Aug-2019 20:21:05 | ---> 46f6d1fdf076 |
| 17-Aug-2019 20:21:05 | Step 3/11 : ENV RABBITMQ_URI="" RABBITMQ_EXCHANGE="clowder" RABBITMQ_VHOST="%2F" RABBITMQ_QUEUE="ncsa.msc.MonitorExtractor" MONGO_URI="" DB_USERNAME="" DB_PASSWORD="" MAIN_SCRIPT="extractor-Monitor.py" |
| 17-Aug-2019 20:21:05 | ---> Running in 83f1181c0307 |
| 17-Aug-2019 20:21:06 | Removing intermediate container 83f1181c0307 |
| 17-Aug-2019 20:21:06 | ---> 4a22d5bfe6c8 |
| 17-Aug-2019 20:21:06 | Step 4/11 : USER root |
| 17-Aug-2019 20:21:06 | ---> Running in 24f3218652a4 |
| 17-Aug-2019 20:21:06 | Removing intermediate container 24f3218652a4 |
| 17-Aug-2019 20:21:06 | ---> f9d027cb844d |
| 17-Aug-2019 20:21:06 | Step 5/11 : COPY requirements.txt /home/clowder/ |
| 17-Aug-2019 20:21:07 | ---> 5fc609d2b96d |
| 17-Aug-2019 20:21:07 | Step 6/11 : RUN pip install --upgrade pip |
| 17-Aug-2019 20:21:08 | ---> Running in 201f014c871c |
| 17-Aug-2019 20:21:10 | Collecting pip |
| 17-Aug-2019 20:21:10 | Downloading https://files.pythonhosted.org/packages/8d/07/f7d7ced2f97ca3098c16565efbe6b15fafcba53e8d9bdb431e09140514b0/pip-19.2.2-py2.py3-none-any.whl (1.4MB) |
| 17-Aug-2019 20:21:10 | Installing collected packages: pip |
| 17-Aug-2019 20:21:10 | Found existing installation: pip 8.1.1 |
| 17-Aug-2019 20:21:10 | Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr |
| 17-Aug-2019 20:21:11 | Successfully installed pip-19.2.2 |
| 17-Aug-2019 20:21:13 | Removing intermediate container 201f014c871c |
| 17-Aug-2019 20:21:13 | ---> 61efa874323c |
| 17-Aug-2019 20:21:13 | Step 7/11 : RUN pip install -r /home/clowder/requirements.txt |
| 17-Aug-2019 20:21:13 | ---> Running in 29c902e849ca |
| 17-Aug-2019 20:21:15 | DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support |
| 17-Aug-2019 20:21:15 | Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) (1.2.1) |
| 17-Aug-2019 20:21:15 | Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2)) |
| 17-Aug-2019 20:21:15 | Downloading https://files.pythonhosted.org/packages/96/53/3782b6cc03500c0949a7ba9dba0c70da95d63d0ed4a04446123987ff983f/openpyxl-1.6.2.tar.gz (199kB) |
| 17-Aug-2019 20:21:15 | Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3)) |
| 17-Aug-2019 20:21:15 | Downloading https://files.pythonhosted.org/packages/2b/5b/4c5b6eafc63e0985b926267579a1e2534af70df0a45932f0c23fcc5f1b88/pika-0.9.14.tar.gz (72kB) |
| 17-Aug-2019 20:21:15 | Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4)) |
| 17-Aug-2019 20:21:16 | Downloading https://files.pythonhosted.org/packages/d7/94/9aa9ddd3e885caa307c0db8af5a1f5d266d3db44e1ae89bd4e14841ab8d0/pymongo-3.2.1.tar.gz (647kB) |
| 17-Aug-2019 20:21:16 | Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5)) |
| 17-Aug-2019 20:21:17 | Downloading https://files.pythonhosted.org/packages/e2/8d/af599c0388f46775c6b039d8b9c4acda2f6ef86787312a35291fff4cb7ca/pytz-2014.3.tar.bz2 (158kB) |
| 17-Aug-2019 20:21:17 | Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6)) |
| 17-Aug-2019 20:21:17 | Downloading https://files.pythonhosted.org/packages/7d/15/6efffc6aee666e1456852c2bf1d483b46bf971a2d509b35a98fc3eae1c60/requests-2.2.1-py2.py3-none-any.whl (625kB) |
| 17-Aug-2019 20:21:17 | Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) (0.1.2) |
| 17-Aug-2019 20:21:17 | Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8)) |
| 17-Aug-2019 20:21:17 | Downloading https://files.pythonhosted.org/packages/b1/13/6fbcb55fef0b34c70cb3753741eaafc0e91553a1318653587a7d145caf15/xlrd-0.9.3.tar.gz (178kB) |
| 17-Aug-2019 20:21:18 | Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd |
| 17-Aug-2019 20:21:18 | Running setup.py install for openpyxl: started |
| 17-Aug-2019 20:21:18 | Running setup.py install for openpyxl: finished with status 'done' |
| 17-Aug-2019 20:21:18 | Found existing installation: pika 0.11.0 |
| 17-Aug-2019 20:21:18 | Uninstalling pika-0.11.0: |
| 17-Aug-2019 20:21:18 | Successfully uninstalled pika-0.11.0 |
| 17-Aug-2019 20:21:18 | Running setup.py install for pika: started |
| 17-Aug-2019 20:21:18 | Running setup.py install for pika: finished with status 'done' |
| 17-Aug-2019 20:21:18 | Running setup.py install for pymongo: started |
| 17-Aug-2019 20:21:19 | Running setup.py install for pymongo: finished with status 'done' |
| 17-Aug-2019 20:21:19 | Running setup.py install for pytz: started |
| 17-Aug-2019 20:21:19 | Running setup.py install for pytz: finished with status 'done' |
| 17-Aug-2019 20:21:19 | Found existing installation: requests 2.18.4 |
| 17-Aug-2019 20:21:19 | Uninstalling requests-2.18.4: |
| 17-Aug-2019 20:21:19 | Successfully uninstalled requests-2.18.4 |
| 17-Aug-2019 20:21:20 | Running setup.py install for xlrd: started |
| 17-Aug-2019 20:21:20 | Running setup.py install for xlrd: finished with status 'done' |
| 17-Aug-2019 20:21:20 | Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3 |
| 17-Aug-2019 20:21:21 | Removing intermediate container 29c902e849ca |
| 17-Aug-2019 20:21:21 | ---> 2930d34bd461 |
| 17-Aug-2019 20:21:21 | Step 8/11 : USER clowder |
| 17-Aug-2019 20:21:22 | ---> Running in a6b1f380c334 |
| 17-Aug-2019 20:21:23 | Removing intermediate container a6b1f380c334 |
| 17-Aug-2019 20:21:23 | ---> 9eebc2194b25 |
| 17-Aug-2019 20:21:23 | Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/ |
| 17-Aug-2019 20:21:24 | ---> a05a484be24d |
| 17-Aug-2019 20:21:24 | Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"] |
| 17-Aug-2019 20:21:24 | ---> Running in 15f144599bbb |
| 17-Aug-2019 20:21:24 | Removing intermediate container 15f144599bbb |
| 17-Aug-2019 20:21:24 | ---> aaf0de8444ed |
| 17-Aug-2019 20:21:24 | Step 11/11 : CMD ["extractor"] |
| 17-Aug-2019 20:21:24 | ---> Running in 2028900bdc16 |
| 17-Aug-2019 20:21:25 | Removing intermediate container 2028900bdc16 |
| 17-Aug-2019 20:21:25 | ---> d8cb999f0f94 |
| 17-Aug-2019 20:21:25 | Successfully built d8cb999f0f94 |
| 17-Aug-2019 20:21:25 | Successfully tagged 5903:latest |
| 17-Aug-2019 20:21:25 | The push refers to repository [docker.io/clowder/extractors-msc-monitor] |
| 17-Aug-2019 20:21:25 | 77a9f3189e94: Preparing |
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| 17-Aug-2019 20:21:26 | 0cdb02ac1d86: Layer already exists |
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| 17-Aug-2019 20:21:27 | ae296cdea338: Pushed |
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| 17-Aug-2019 20:21:27 | c56153825175: Layer already exists |
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| 17-Aug-2019 20:21:28 | 2889adc23b49: Pushed |
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| 17-Aug-2019 20:21:30 | browndog_v0.2.0: digest: sha256:04c8eb77fee9504f2483ea88cf0f852070113741ca933bf855dc66fe69d6a186 size: 3031 |
| 17-Aug-2019 20:21:30 | The push refers to repository [docker.io/clowder/extractors-msc-monitor] |
| 17-Aug-2019 20:21:30 | 77a9f3189e94: Preparing |
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| 17-Aug-2019 20:21:31 | 2889adc23b49: Layer already exists |
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| 17-Aug-2019 20:21:32 | browndog_v0.3.0: digest: sha256:04c8eb77fee9504f2483ea88cf0f852070113741ca933bf855dc66fe69d6a186 size: 3031 |
| 17-Aug-2019 20:21:32 | The push refers to repository [docker.io/clowder/extractors-msc-monitor] |
| 17-Aug-2019 20:21:32 | 77a9f3189e94: Preparing |
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| 17-Aug-2019 20:21:32 | ae620432889d: Preparing |
| 17-Aug-2019 20:21:32 | a2022691bf95: Preparing |
| 17-Aug-2019 20:21:32 | 7f7a065d245a: Waiting |
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| 17-Aug-2019 20:21:32 | a2022691bf95: Waiting |
| 17-Aug-2019 20:21:32 | f2297bdfc824: Waiting |
| 17-Aug-2019 20:21:32 | 0fbe2bcb1bf9: Waiting |
| 17-Aug-2019 20:21:32 | 59669fcdd5eb: Waiting |
| 17-Aug-2019 20:21:33 | 77a9f3189e94: Layer already exists |
| 17-Aug-2019 20:21:33 | ae296cdea338: Layer already exists |
| 17-Aug-2019 20:21:33 | 0cdb02ac1d86: Layer already exists |
| 17-Aug-2019 20:21:33 | 2889adc23b49: Layer already exists |
| 17-Aug-2019 20:21:33 | e60a00ae94f1: Layer already exists |
| 17-Aug-2019 20:21:33 | 59669fcdd5eb: Layer already exists |
| 17-Aug-2019 20:21:33 | f96e6b25195f: Layer already exists |
| 17-Aug-2019 20:21:33 | 0fbe2bcb1bf9: Layer already exists |
| 17-Aug-2019 20:21:33 | f2297bdfc824: Layer already exists |
| 17-Aug-2019 20:21:33 | 7f7a065d245a: Layer already exists |
| 17-Aug-2019 20:21:33 | c56153825175: Layer already exists |
| 17-Aug-2019 20:21:33 | ae620432889d: Layer already exists |
| 17-Aug-2019 20:21:33 | a2022691bf95: Layer already exists |
| 17-Aug-2019 20:21:34 | latest: digest: sha256:04c8eb77fee9504f2483ea88cf0f852070113741ca933bf855dc66fe69d6a186 size: 3031 |
| 17-Aug-2019 20:21:34 | Untagged: 5903:latest |
| 17-Aug-2019 20:21:34 | Sending build context to Docker daemon 12.1MB |
| 17-Aug-2019 20:21:34 | |
| 17-Aug-2019 20:21:34 | Step 1/11 : FROM clowder/pyclowder:1 |
| 17-Aug-2019 20:21:34 | ---> d1a9e970ed30 |
| 17-Aug-2019 20:21:34 | Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu> |
| 17-Aug-2019 20:21:34 | ---> Using cache |
| 17-Aug-2019 20:21:34 | ---> 46f6d1fdf076 |
| 17-Aug-2019 20:21:34 | Step 3/11 : ENV RABBITMQ_URI="" RABBITMQ_EXCHANGE="clowder" RABBITMQ_VHOST="%2F" RABBITMQ_QUEUE="ncsa.msc.PhenotypeExtractor" MONGO_URI="" DB_USERNAME="" DB_PASSWORD="" MAIN_SCRIPT="extractor-Phenotype.py" |
| 17-Aug-2019 20:21:34 | ---> Running in 0ada6c9aa74f |
| 17-Aug-2019 20:21:35 | Removing intermediate container 0ada6c9aa74f |
| 17-Aug-2019 20:21:35 | ---> f6ceb84b37bf |
| 17-Aug-2019 20:21:35 | Step 4/11 : USER root |
| 17-Aug-2019 20:21:35 | ---> Running in 326d062a2d6a |
| 17-Aug-2019 20:21:35 | Removing intermediate container 326d062a2d6a |
| 17-Aug-2019 20:21:35 | ---> c0109ad8ecf8 |
| 17-Aug-2019 20:21:35 | Step 5/11 : COPY requirements.txt /home/clowder/ |
| 17-Aug-2019 20:21:35 | ---> d2af425a8c36 |
| 17-Aug-2019 20:21:35 | Step 6/11 : RUN pip install --upgrade pip |
| 17-Aug-2019 20:21:36 | ---> Running in 920ff5016ecd |
| 17-Aug-2019 20:21:37 | Collecting pip |
| 17-Aug-2019 20:21:38 | Downloading https://files.pythonhosted.org/packages/8d/07/f7d7ced2f97ca3098c16565efbe6b15fafcba53e8d9bdb431e09140514b0/pip-19.2.2-py2.py3-none-any.whl (1.4MB) |
| 17-Aug-2019 20:21:38 | Installing collected packages: pip |
| 17-Aug-2019 20:21:38 | Found existing installation: pip 8.1.1 |
| 17-Aug-2019 20:21:38 | Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr |
| 17-Aug-2019 20:21:39 | Successfully installed pip-19.2.2 |
| 17-Aug-2019 20:21:40 | Removing intermediate container 920ff5016ecd |
| 17-Aug-2019 20:21:40 | ---> 4240500ecb9c |
| 17-Aug-2019 20:21:40 | Step 7/11 : RUN pip install -r /home/clowder/requirements.txt |
| 17-Aug-2019 20:21:40 | ---> Running in 30745a23ac35 |
| 17-Aug-2019 20:21:41 | DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support |
| 17-Aug-2019 20:21:41 | Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1)) (1.2.1) |
| 17-Aug-2019 20:21:41 | Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2)) |
| 17-Aug-2019 20:21:41 | Downloading https://files.pythonhosted.org/packages/96/53/3782b6cc03500c0949a7ba9dba0c70da95d63d0ed4a04446123987ff983f/openpyxl-1.6.2.tar.gz (199kB) |
| 17-Aug-2019 20:21:42 | Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3)) |
| 17-Aug-2019 20:21:42 | Downloading https://files.pythonhosted.org/packages/2b/5b/4c5b6eafc63e0985b926267579a1e2534af70df0a45932f0c23fcc5f1b88/pika-0.9.14.tar.gz (72kB) |
| 17-Aug-2019 20:21:42 | Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4)) |
| 17-Aug-2019 20:21:43 | Downloading https://files.pythonhosted.org/packages/d7/94/9aa9ddd3e885caa307c0db8af5a1f5d266d3db44e1ae89bd4e14841ab8d0/pymongo-3.2.1.tar.gz (647kB) |
| 17-Aug-2019 20:21:43 | Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5)) |
| 17-Aug-2019 20:21:43 | Downloading https://files.pythonhosted.org/packages/e2/8d/af599c0388f46775c6b039d8b9c4acda2f6ef86787312a35291fff4cb7ca/pytz-2014.3.tar.bz2 (158kB) |
| 17-Aug-2019 20:21:44 | Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6)) |
| 17-Aug-2019 20:21:44 | Downloading https://files.pythonhosted.org/packages/7d/15/6efffc6aee666e1456852c2bf1d483b46bf971a2d509b35a98fc3eae1c60/requests-2.2.1-py2.py3-none-any.whl (625kB) |
| 17-Aug-2019 20:21:44 | Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7)) (0.1.2) |
| 17-Aug-2019 20:21:44 | Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8)) |
| 17-Aug-2019 20:21:44 | Downloading https://files.pythonhosted.org/packages/b1/13/6fbcb55fef0b34c70cb3753741eaafc0e91553a1318653587a7d145caf15/xlrd-0.9.3.tar.gz (178kB) |
| 17-Aug-2019 20:21:44 | Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd |
| 17-Aug-2019 20:21:44 | Running setup.py install for openpyxl: started |
| 17-Aug-2019 20:21:45 | Running setup.py install for openpyxl: finished with status 'done' |
| 17-Aug-2019 20:21:45 | Found existing installation: pika 0.11.0 |
| 17-Aug-2019 20:21:45 | Uninstalling pika-0.11.0: |
| 17-Aug-2019 20:21:45 | Successfully uninstalled pika-0.11.0 |
| 17-Aug-2019 20:21:45 | Running setup.py install for pika: started |
| 17-Aug-2019 20:21:45 | Running setup.py install for pika: finished with status 'done' |
| 17-Aug-2019 20:21:45 | Running setup.py install for pymongo: started |
| 17-Aug-2019 20:21:45 | Running setup.py install for pymongo: finished with status 'done' |
| 17-Aug-2019 20:21:45 | Running setup.py install for pytz: started |
| 17-Aug-2019 20:21:46 | Running setup.py install for pytz: finished with status 'done' |
| 17-Aug-2019 20:21:46 | Found existing installation: requests 2.18.4 |
| 17-Aug-2019 20:21:46 | Uninstalling requests-2.18.4: |
| 17-Aug-2019 20:21:46 | Successfully uninstalled requests-2.18.4 |
| 17-Aug-2019 20:21:46 | Running setup.py install for xlrd: started |
| 17-Aug-2019 20:21:47 | Running setup.py install for xlrd: finished with status 'done' |
| 17-Aug-2019 20:21:47 | Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3 |
| 17-Aug-2019 20:21:49 | Removing intermediate container 30745a23ac35 |
| 17-Aug-2019 20:21:49 | ---> 1797dde8f847 |
| 17-Aug-2019 20:21:49 | Step 8/11 : USER clowder |
| 17-Aug-2019 20:21:49 | ---> Running in 19deddab843e |
| 17-Aug-2019 20:21:49 | Removing intermediate container 19deddab843e |
| 17-Aug-2019 20:21:49 | ---> c193e004c918 |
| 17-Aug-2019 20:21:49 | Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/ |
| 17-Aug-2019 20:21:51 | ---> a6a9b3729b73 |
| 17-Aug-2019 20:21:51 | Step 10/11 : ENTRYPOINT ["/home/clowder/entrypoint.sh"] |
| 17-Aug-2019 20:21:51 | ---> Running in 7b16d43a738a |
| 17-Aug-2019 20:21:52 | Removing intermediate container 7b16d43a738a |
| 17-Aug-2019 20:21:52 | ---> fe8b5bf4a7c9 |
| 17-Aug-2019 20:21:52 | Step 11/11 : CMD ["extractor"] |
| 17-Aug-2019 20:21:52 | ---> Running in 8d40e84f64b6 |
| 17-Aug-2019 20:21:53 | Removing intermediate container 8d40e84f64b6 |
| 17-Aug-2019 20:21:53 | ---> eec26e3fc5b7 |
| 17-Aug-2019 20:21:53 | Successfully built eec26e3fc5b7 |
| 17-Aug-2019 20:21:53 | Successfully tagged 5903:latest |
| 17-Aug-2019 20:21:53 | The push refers to repository [docker.io/clowder/extractors-msc-phenotype] |
| 17-Aug-2019 20:21:53 | 8bec6f89fe17: Preparing |
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| 17-Aug-2019 20:21:54 | 0cdb02ac1d86: Layer already exists |
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| 17-Aug-2019 20:21:55 | 8bec6f89fe17: Pushed |
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| 17-Aug-2019 20:21:55 | ae620432889d: Layer already exists |
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| 17-Aug-2019 20:21:56 | 84f606e1b641: Pushed |
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| 17-Aug-2019 20:21:59 | browndog_v0.2.0: digest: sha256:062091ca4c1cd318f2c45de8439012781be496c5110a07abc234f53097a293fc size: 3031 |
| 17-Aug-2019 20:21:59 | The push refers to repository [docker.io/clowder/extractors-msc-phenotype] |
| 17-Aug-2019 20:21:59 | 8bec6f89fe17: Preparing |
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| 17-Aug-2019 20:21:59 | 84f606e1b641: Layer already exists |
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| 17-Aug-2019 20:22:00 | browndog_v0.3.0: digest: sha256:062091ca4c1cd318f2c45de8439012781be496c5110a07abc234f53097a293fc size: 3031 |
| 17-Aug-2019 20:22:01 | The push refers to repository [docker.io/clowder/extractors-msc-phenotype] |
| 17-Aug-2019 20:22:01 | 8bec6f89fe17: Preparing |
| 17-Aug-2019 20:22:01 | 84f606e1b641: Preparing |
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| 17-Aug-2019 20:22:02 | a2022691bf95: Layer already exists |
| 17-Aug-2019 20:22:02 | latest: digest: sha256:062091ca4c1cd318f2c45de8439012781be496c5110a07abc234f53097a293fc size: 3031 |
| 17-Aug-2019 20:22:02 | Untagged: 5903:latest |
| 17-Aug-2019 20:22:02 | Finished task 'docker build' with result: Success |
| 17-Aug-2019 20:22:02 | Running post build plugin 'Docker Container Cleanup' |
| 17-Aug-2019 20:22:02 | Running post build plugin 'NCover Results Collector' |
| 17-Aug-2019 20:22:02 | Running post build plugin 'Clover Results Collector' |
| 17-Aug-2019 20:22:02 | Running post build plugin 'npm Cache Cleanup' |
| 17-Aug-2019 20:22:02 | Running post build plugin 'Artifact Copier' |
| 17-Aug-2019 20:22:02 | Finalising the build... |
| 17-Aug-2019 20:22:02 | Stopping timer. |
| 17-Aug-2019 20:22:02 | Build CATS-MSC-JOB1-40 completed. |
| 17-Aug-2019 20:22:02 | Running on server: post build plugin 'NCover Results Collector' |
| 17-Aug-2019 20:22:02 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 17-Aug-2019 20:22:02 | Running on server: post build plugin 'Clover Delta Calculator' |
| 17-Aug-2019 20:22:02 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 17-Aug-2019 20:22:02 | All post build plugins have finished |
| 17-Aug-2019 20:22:02 | Generating build results summary... |
| 17-Aug-2019 20:22:02 | Saving build results to disk... |
| 17-Aug-2019 20:22:02 | Logging substituted variables... |
| 17-Aug-2019 20:22:02 | Indexing build results... |
| 17-Aug-2019 20:22:02 | Finished building CATS-MSC-JOB1-40. |