Console Output

Started by GitHub push by s-fong
Started by user David Nickerson
Rebuilds build #151
Running as SYSTEM
Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite
The recommended git tool is: NONE
No credentials specified
Wiping out workspace first.
Cloning the remote Git repository
Cloning repository https://github.com/Physiome/journal-website
 > git init /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite # timeout=10
Fetching upstream changes from https://github.com/Physiome/journal-website
 > git --version # timeout=10
 > git --version # 'git version 2.17.1'
 > git fetch --tags --progress -- https://github.com/Physiome/journal-website +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/Physiome/journal-website # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
 > git rev-parse refs/remotes/origin/journaldev^{commit} # timeout=10
Checking out Revision 337ead1dbcfb341f0072410772cda881e48835c9 (refs/remotes/origin/journaldev)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 337ead1dbcfb341f0072410772cda881e48835c9 # timeout=10
Commit message: "Merge pull request #171 from Physiome/nickerso-patch-1"
 > git rev-list --no-walk 337ead1dbcfb341f0072410772cda881e48835c9 # timeout=10
[Set GitHub commit status (universal)] PENDING on repos [] (sha:337ead1) with context:journaldev-build
[PhysiomeJournalDevelopmentSite] $ /usr/bin/python3.7 /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9
Using base prefix '/usr'
New python executable in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/bin/python3.7
Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/bin/python
Installing setuptools, pip, wheel...done.
/home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenv.py:1041: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
  import imp
[PhysiomeJournalDevelopmentSite] $ /bin/sh -xe /tmp/shiningpanda376593996535239823.sh
+ make deps
pip install -r py-requirements.txt
Collecting pelican>3.6
  Using cached pelican-4.7.2-py3-none-any.whl (1.4 MB)
Collecting markdown
  Using cached Markdown-3.3.6-py3-none-any.whl (97 kB)
Collecting pygments>=2.6
  Using cached Pygments-2.11.2-py3-none-any.whl (1.1 MB)
Collecting unidecode>=1.1
  Using cached Unidecode-1.3.4-py3-none-any.whl (235 kB)
Collecting blinker>=1.4
  Using cached blinker-1.4-py3-none-any.whl
Collecting feedgenerator>=1.9
  Using cached feedgenerator-2.0.0-py3-none-any.whl (21 kB)
Collecting python-dateutil>=2.8
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting pytz>=2020.1
  Using cached pytz-2022.1-py2.py3-none-any.whl (503 kB)
Collecting docutils>=0.16
  Using cached docutils-0.18.1-py2.py3-none-any.whl (570 kB)
Collecting jinja2>=2.7
  Downloading Jinja2-3.1.1-py3-none-any.whl (132 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.6/132.6 KB 9.2 MB/s eta 0:00:00
Collecting rich>=10.1
  Using cached rich-12.0.1-py3-none-any.whl (224 kB)
Collecting importlib-metadata>=4.4
  Using cached importlib_metadata-4.11.3-py3-none-any.whl (18 kB)
Collecting zipp>=0.5
  Using cached zipp-3.7.0-py3-none-any.whl (5.3 kB)
Collecting typing-extensions>=3.6.4
  Using cached typing_extensions-4.1.1-py3-none-any.whl (26 kB)
Collecting MarkupSafe>=2.0
  Using cached MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting six>=1.5
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting commonmark<0.10.0,>=0.9.0
  Using cached commonmark-0.9.1-py2.py3-none-any.whl (51 kB)
Installing collected packages: pytz, commonmark, blinker, zipp, unidecode, typing-extensions, six, pygments, MarkupSafe, feedgenerator, docutils, rich, python-dateutil, jinja2, importlib-metadata, pelican, markdown
Successfully installed MarkupSafe-2.1.1 blinker-1.4 commonmark-0.9.1 docutils-0.18.1 feedgenerator-2.0.0 importlib-metadata-4.11.3 jinja2-3.1.1 markdown-3.3.6 pelican-4.7.2 pygments-2.11.2 python-dateutil-2.8.2 pytz-2022.1 rich-12.0.1 six-1.16.0 typing-extensions-4.1.1 unidecode-1.3.4 zipp-3.7.0
+ make html
pelican /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite/content -o /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite/output -s /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite/pelicanconf.py 
Done: Processed 12 articles, 0 drafts, 0 hidden articles, 9 pages, 0 hidden 
pages and 0 draft pages in 0.51 seconds.
+ scp -v -2 -r -o GlobalKnownHostsFile=**** -i **** output/about.html output/archive-descriptions output/archives.html output/article-prototypes.html output/articles output/author output/authors.html output/categories.html output/contact-us.html output/data output/editorial-board.html output/faqs.html output/index.html output/instructions-to-authors.html output/models output/pdfs output/physiome-project.html output/pmr.html output/tags.html output/testing.html output/theme pj-site@abiwebsrv02.bioeng.auckland.ac.nz:/home/pj-site/journaldev.physiomeproject.org/
Executing: program /usr/bin/ssh host abiwebsrv02.bioeng.auckland.ac.nz, user pj-site, command scp -v -r -d -t /home/pj-site/journaldev.physiomeproject.org/
OpenSSH_7.6p1 Ubuntu-4ubuntu0.5, OpenSSL 1.0.2n  7 Dec 2017
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 19: Applying options for *
debug1: Connecting to abiwebsrv02.bioeng.auckland.ac.nz [130.216.230.134] port 22.
debug1: Connection established.
debug1: key_load_public: No such file or directory
debug1: identity file **** type -1
debug1: key_load_public: No such file or directory
debug1: identity file ****-cert type -1
debug1: Local version string SSH-2.0-OpenSSH_7.6p1 Ubuntu-4ubuntu0.5
debug1: Remote protocol version 2.0, remote software version OpenSSH_8.2p1 Ubuntu-4ubuntu0.4
debug1: match: OpenSSH_8.2p1 Ubuntu-4ubuntu0.4 pat OpenSSH* compat 0x04000000
debug1: Authenticating to abiwebsrv02.bioeng.auckland.ac.nz:22 as 'pj-site'
debug1: SSH2_MSG_KEXINIT sent
debug1: SSH2_MSG_KEXINIT received
debug1: kex: algorithm: curve25519-sha256
debug1: kex: host key algorithm: ecdsa-sha2-nistp256
debug1: kex: server->client cipher: chacha20-poly1305@openssh.com MAC: <implicit> compression: none
debug1: kex: client->server cipher: chacha20-poly1305@openssh.com MAC: <implicit> compression: none
debug1: expecting SSH2_MSG_KEX_ECDH_REPLY
debug1: Server host key: ecdsa-sha2-nistp256 SHA256:nrl+uVNnKBIgl3yLEOD5DNhwRjwUUYwcQfwVtvox6as
debug1: Host 'abiwebsrv02.bioeng.auckland.ac.nz' is known and matches the ECDSA host key.
debug1: Found key in /home/cmiss/.ssh/known_hosts:9
debug1: rekey after 134217728 blocks
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug1: SSH2_MSG_NEWKEYS received
debug1: rekey after 134217728 blocks
debug1: SSH2_MSG_EXT_INFO received
debug1: kex_input_ext_info: server-sig-algs=<ssh-ed25519,sk-ssh-ed25519@openssh.com,ssh-rsa,rsa-sha2-256,rsa-sha2-512,ssh-dss,ecdsa-sha2-nistp256,ecdsa-sha2-nistp384,ecdsa-sha2-nistp521,sk-ecdsa-sha2-nistp256@openssh.com>
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug1: Authentications that can continue: publickey,password
debug1: Next authentication method: publickey
debug1: Trying private key: ****
debug1: Authentication succeeded (publickey).
Authenticated to abiwebsrv02.bioeng.auckland.ac.nz ([130.216.230.134]:22).
debug1: channel 0: new [client-session]
debug1: Requesting no-more-sessions@openssh.com
debug1: Entering interactive session.
debug1: pledge: network
debug1: client_input_global_request: rtype hostkeys-00@openssh.com want_reply 0
debug1: Remote: /home/pj-site/.ssh/authorized_keys:1: key options: agent-forwarding port-forwarding pty user-rc x11-forwarding
debug1: Sending environment.
debug1: Sending env LANG = en_NZ.UTF-8
debug1: Sending command: scp -v -r -d -t /home/pj-site/journaldev.physiomeproject.org/
Sending file modes: C0664 19801 about.html
Sink: C0664 19801 about.html
Entering directory: D0775 0 archive-descriptions
Sink: D0775 0 archive-descriptions
Sending file modes: C0664 3076 test2.json
Sink: C0664 3076 test2.json
Sink: E
Sending file modes: C0664 9621 archives.html
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Sending file modes: C0664 10191 article-prototypes.html
Sink: C0664 10191 article-prototypes.html
Entering directory: D0775 0 articles
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Sending file modes: C0664 22833 index.html
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Entering directory: D0775 0 10.36903
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Sending file modes: C0664 17280 physiome.12871364.html
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Sending file modes: C0664 20855 physiome.16550526.html
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Sending file modes: C0664 17573 physiome.13034423.html
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Sink: E
Sink: E
Entering directory: D0775 0 author
Sending file modes: C0664 17978 the-physiome-project.html
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Sink: E
Sending file modes: C0664 9621 authors.html
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Sending file modes: C0664 9621 categories.html
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Sending file modes: C0664 9919 contact-us.html
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Entering directory: D0775 0 data
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Sending file modes: C0664 625571 nickerson-and-noble-1962.csv
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Sink: E
Sending file modes: C0664 14806 editorial-board.html
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Sending file modes: C0664 16116 faqs.html
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Sending file modes: C0664 17978 index.html
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Sending file modes: C0664 28426 instructions-to-authors.html
Sink: C0664 28426 instructions-to-authors.html
Entering directory: D0775 0 models
Sink: D0775 0 models
Entering directory: D0775 0 ccm
Sending file modes: C0664 449150 nerves_2.json
Sink: D0775 0 ccm
Sink: C0664 449150 nerves_2.json
Sending file modes: C0664 201 jaw_1.json
Sink: C0664 201 jaw_1.json
Sending file modes: C0664 161 jaw_view.json
Sink: C0664 161 jaw_view.json
Sending file modes: C0664 174 nerves_1.json
Sink: C0664 174 nerves_1.json
Sending file modes: C0664 3156133 jaw_2.json
Sink: C0664 3156133 jaw_2.json
Sink: E
Sink: E
Entering directory: D0775 0 pdfs
Sink: D0775 0 pdfs
Sending file modes: C0664 772737 A model of pH control v4.pdf
Sink: C0664 772737 A model of pH control v4.pdf
Sink: E
Sending file modes: C0664 10817 physiome-project.html
Sink: C0664 10817 physiome-project.html
Sending file modes: C0664 10160 pmr.html
Sink: C0664 10160 pmr.html
Sending file modes: C0664 9621 tags.html
Sink: C0664 9621 tags.html
Sending file modes: C0664 10490 testing.html
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Entering directory: D0775 0 theme
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Entering directory: D0775 0 js
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Sending file modes: C0664 257551 jquery.js
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Sending file modes: C0664 0 andre.js
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Sending file modes: C0664 8663 what-input.js
Sink: C0664 8663 what-input.js
Entering directory: D0775 0 models
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Sending file modes: C0664 524257 three.min.js
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Sending file modes: C0664 48448 zinc_3js_renderer.js
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Sending file modes: C0664 35330 zinc_threejs_control.js
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Sink: E
Sending file modes: C0664 123510 foundation.min.js
Sink: C0664 123510 foundation.min.js
Sending file modes: C0664 333138 foundation.js
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Entering directory: D0775 0 views
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Sending file modes: C0664 1928 cellml.js
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Sending file modes: C0664 3673 sedml.js
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Sink: E
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Entering directory: D0775 0 css
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Sending file modes: C0664 0 app.css
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Entering directory: D0775 0 foundation-icons
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Sink: E
debug1: client_input_channel_req: channel 0 rtype exit-status reply 0
debug1: channel 0: free: client-session, nchannels 1
debug1: fd 0 clearing O_NONBLOCK
debug1: fd 1 clearing O_NONBLOCK
debug1: fd 2 clearing O_NONBLOCK
Transferred: sent 24691220, received 45484 bytes, in 1.9 seconds
Bytes per second: sent 13055164.7, received 24049.1
debug1: Exit status 0
[Set GitHub commit status (universal)] SUCCESS on repos [] (sha:337ead1) with context:journaldev-build
Finished: SUCCESS