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Started by GitHub push by nickerso
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 2.25.1'
 > git fetch --tags --force --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 223eefc6b30c5855451e9beae21873e639e03593 (refs/remotes/origin/journaldev)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 223eefc6b30c5855451e9beae21873e639e03593 # timeout=10
Commit message: "Removing empty author list"
 > git rev-list --no-walk 71aaafb170b3a1ada9d15d5945a6aa80b24865b0 # timeout=10
[Set GitHub commit status (universal)] PENDING on repos [] (sha:223eefc) 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/shiningpanda9621975366473728912.sh
+ make deps
pip install -r py-requirements.txt
Collecting pelican>3.6
  Using cached pelican-4.8.0-py3-none-any.whl (1.4 MB)
Collecting markdown
  Using cached Markdown-3.4.1-py3-none-any.whl (93 kB)
Collecting blinker>=1.4
  Using cached blinker-1.5-py2.py3-none-any.whl (12 kB)
Collecting python-dateutil>=2.8
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting unidecode>=1.1
  Using cached Unidecode-1.3.6-py3-none-any.whl (235 kB)
Collecting feedgenerator>=1.9
  Using cached feedgenerator-2.0.0-py3-none-any.whl (21 kB)
Collecting jinja2>=2.7
  Using cached Jinja2-3.1.2-py3-none-any.whl (133 kB)
Collecting pygments>=2.6
  Using cached Pygments-2.14.0-py3-none-any.whl (1.1 MB)
Collecting pytz>=2020.1
  Using cached pytz-2022.7.1-py2.py3-none-any.whl (499 kB)
Collecting rich>=10.1
  Using cached rich-13.2.0-py3-none-any.whl (238 kB)
Collecting docutils>=0.16
  Using cached docutils-0.19-py3-none-any.whl (570 kB)
Collecting importlib-metadata>=4.4
  Using cached importlib_metadata-6.0.0-py3-none-any.whl (21 kB)
Collecting zipp>=0.5
  Using cached zipp-3.11.0-py3-none-any.whl (6.6 kB)
Collecting typing-extensions>=3.6.4
  Using cached typing_extensions-4.4.0-py3-none-any.whl (26 kB)
Collecting MarkupSafe>=2.0
  Using cached MarkupSafe-2.1.2-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 markdown-it-py<3.0.0,>=2.1.0
  Using cached markdown_it_py-2.1.0-py3-none-any.whl (84 kB)
Collecting mdurl~=0.1
  Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Installing collected packages: pytz, zipp, unidecode, typing-extensions, six, pygments, mdurl, MarkupSafe, feedgenerator, docutils, blinker, python-dateutil, markdown-it-py, jinja2, importlib-metadata, rich, markdown, pelican
Successfully installed MarkupSafe-2.1.2 blinker-1.5 docutils-0.19 feedgenerator-2.0.0 importlib-metadata-6.0.0 jinja2-3.1.2 markdown-3.4.1 markdown-it-py-2.1.0 mdurl-0.1.2 pelican-4.8.0 pygments-2.14.0 python-dateutil-2.8.2 pytz-2022.7.1 rich-13.2.0 six-1.16.0 typing-extensions-4.4.0 unidecode-1.3.6 zipp-3.11.0
+ 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 16 articles, 0 drafts, 0 hidden articles, 9 pages, 0 hidden 
pages and 0 draft pages in 0.53 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_8.2p1 Ubuntu-4ubuntu0.5, OpenSSL 1.1.1f  31 Mar 2020
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 19: include /etc/ssh/ssh_config.d/*.conf matched no files
debug1: /etc/ssh/ssh_config line 21: Applying options for *
debug1: Connecting to abiwebsrv02.bioeng.auckland.ac.nz [130.216.230.134] port 22.
debug1: Connection established.
debug1: identity file **** type -1
debug1: identity file ****-cert type -1
debug1: Local version string SSH-2.0-OpenSSH_8.2p1 Ubuntu-4ubuntu0.5
debug1: Remote protocol version 2.0, remote software version OpenSSH_8.2p1 Ubuntu-4ubuntu0.5
debug1: match: OpenSSH_8.2p1 Ubuntu-4ubuntu0.5 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 out after 134217728 blocks
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug1: SSH2_MSG_NEWKEYS received
debug1: rekey in after 134217728 blocks
debug1: Will attempt key: ****  explicit
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
Sending file modes: C0664 27920 index.html
Sink: D0775 0 articles
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Entering directory: D0775 0 10.36903
Sink: D0775 0 10.36903
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 18876 physiome.12885590.html
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Sending file modes: C0664 15489 physiome.16828756.html
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Sending file modes: C0664 14733 physiome.21708179.html
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Sending file modes: C0664 17573 physiome.13034423.html
Sink: C0664 17573 physiome.13034423.html
Sink: E
Sink: E
Entering directory: D0775 0 author
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Sending file modes: C0664 19518 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
Sink: C0664 9621 categories.html
Sending file modes: C0664 9919 contact-us.html
Sink: C0664 9919 contact-us.html
Entering directory: D0775 0 data
Sending file modes: C0664 625571 nickerson-and-noble-1962.csv
Sink: D0775 0 data
Sink: C0664 625571 nickerson-and-noble-1962.csv
Sink: E
Sending file modes: C0664 14946 editorial-board.html
Sink: C0664 14946 editorial-board.html
Sending file modes: C0664 16116 faqs.html
Sink: C0664 16116 faqs.html
Sending file modes: C0664 19518 index.html
Sink: C0664 19518 index.html
Sending file modes: C0664 28922 instructions-to-authors.html
Sink: C0664 28922 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 10444 testing.html
Sink: C0664 10444 testing.html
Entering directory: D0775 0 theme
Sink: D0775 0 theme
Entering directory: D0775 0 js
Sink: D0775 0 js
Sending file modes: C0664 257551 jquery.js
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Sending file modes: C0664 0 andre.js
Sink: C0664 0 andre.js
Sending file modes: C0664 8663 what-input.js
Sink: C0664 8663 what-input.js
Entering directory: D0775 0 models
Sink: D0775 0 models
Sending file modes: C0664 524257 three.min.js
Sink: C0664 524257 three.min.js
Sending file modes: C0664 48448 zinc_3js_renderer.js
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Sending file modes: C0664 35330 zinc_threejs_control.js
Sink: C0664 35330 zinc_threejs_control.js
Sink: E
Sending file modes: C0664 123510 foundation.min.js
Sink: C0664 123510 foundation.min.js
Sending file modes: C0664 333138 foundation.js
Sink: C0664 333138 foundation.js
Entering directory: D0775 0 views
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Sending file modes: C0664 1928 cellml.js
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Sink: E
Sink: E
Entering directory: D0775 0 css
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Sending file modes: C0664 0 app.css
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Sending file modes: C0664 110693 foundation.css
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Entering directory: D0775 0 foundation-icons
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Sending file modes: C0664 324210 preview.html
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Sending file modes: C0664 19508 foundation-icons.css
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Sink: C0664 407504 ABI_Positive_RGB.jpg
Sending file modes: C0664 166123 abi-hc-rgb-white.png
Sink: C0664 166123 abi-hc-rgb-white.png
Sending file modes: C0664 38639 iups.svg
Sink: C0664 38639 iups.svg
Sink: E
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 2 clearing O_NONBLOCK
Transferred: sent 24758404, received 45756 bytes, in 1.1 seconds
Bytes per second: sent 21673135.5, received 40054.1
debug1: Exit status 0
[Set GitHub commit status (universal)] SUCCESS on repos [] (sha:223eefc) with context:journaldev-build
Finished: SUCCESS