Started by GitHub push by nickerso
Running as SYSTEM
Building remotely on Ubuntu_16.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/PhysiomeJournalSite
The recommended git tool is: NONE
No credentials specified
> git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
> git config remote.origin.url https://github.com/Physiome/journal-website # 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 rev-parse refs/remotes/origin/master^{commit} # timeout=10
Checking out Revision d6d3d53c2153a6c229a8ed28e3a56c02d1bec34b (refs/remotes/origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f d6d3d53c2153a6c229a8ed28e3a56c02d1bec34b # timeout=10
Commit message: "Merge pull request #105 from Physiome/journaldev"
> git rev-list --no-walk 811d991e8f93b7a3e8b06a52a223d7a88f6f9a73 # timeout=10
[PhysiomeJournalSite] $ /bin/sh -xe /tmp/shiningpanda4604262919111311086.sh
+ make deps
pip install -r py-requirements.txt
Requirement already satisfied: pelican>3.6 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from -r py-requirements.txt (line 1)) (4.6.0)
Requirement already satisfied: markdown in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from -r py-requirements.txt (line 2)) (3.3.4)
Requirement already satisfied: python-dateutil>=2.8 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (2.8.1)
Requirement already satisfied: blinker>=1.4 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (1.4)
Requirement already satisfied: pytz>=2020.1 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (2021.1)
Requirement already satisfied: feedgenerator>=1.9 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (1.9.1)
Requirement already satisfied: unidecode>=1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (1.2.0)
Requirement already satisfied: jinja2>=2.7 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (3.0.1)
Requirement already satisfied: pygments>=2.6 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (2.9.0)
Requirement already satisfied: docutils>=0.16 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (0.17.1)
Requirement already satisfied: six in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from feedgenerator>=1.9->pelican>3.6->-r py-requirements.txt (line 1)) (1.16.0)
Requirement already satisfied: MarkupSafe>=2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from jinja2>=2.7->pelican>3.6->-r py-requirements.txt (line 1)) (2.0.1)
Requirement already satisfied: importlib-metadata in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from markdown->-r py-requirements.txt (line 2)) (4.4.0)
Requirement already satisfied: typing-extensions>=3.6.4 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from importlib-metadata->markdown->-r py-requirements.txt (line 2)) (3.10.0.0)
Requirement already satisfied: zipp>=0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from importlib-metadata->markdown->-r py-requirements.txt (line 2)) (3.4.1)
+ make html
pelican /home/cmiss/Jenkins/workspace/PhysiomeJournalSite/content -o /home/cmiss/Jenkins/workspace/PhysiomeJournalSite/output -s /home/cmiss/Jenkins/workspace/PhysiomeJournalSite/pelicanconf.py
Done: Processed 7 articles, 0 drafts, 7 pages, 0 hidden pages and 0 draft pages in 0.46 seconds.
+ scp -v -2 -r -o GlobalKnownHostsFile=**** -i **** output/about.html output/archive-descriptions output/archives.html output/articles output/articles.html output/author output/authors.html output/categories.html output/data output/editorial-board.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/journal.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/journal.physiomeproject.org/
OpenSSH_7.6p1 Ubuntu-4ubuntu0.3, 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-4ubuntu0.3
debug1: Remote protocol version 2.0, remote software version OpenSSH_7.6p1 Ubuntu-4ubuntu0.4
debug1: match: OpenSSH_7.6p1 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,ssh-rsa,rsa-sha2-256,rsa-sha2-512,ssh-dss,ecdsa-sha2-nistp256,ecdsa-sha2-nistp384,ecdsa-sha2-nistp521>
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: Sending environment.
debug1: Sending env LANG = en_NZ.UTF-8
debug1: Sending command: scp -v -r -d -t /home/pj-site/journal.physiomeproject.org/
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Entering directory: D0775 0 models
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Entering directory: D0775 0 ccm
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Entering directory: D0775 0 pdfs
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Sending file modes: C0664 15599 associated-branding.png
Sink: C0664 15599 associated-branding.png
Sending file modes: C0664 46735 Physiome-under.png
Sink: C0664 46735 Physiome-under.png
Sending file modes: C0664 208237 GoodFigureExample.jpg
Sink: C0664 208237 GoodFigureExample.jpg
Sending file modes: C0664 73088 Physiome-beside-middle.png
Sink: C0664 73088 Physiome-beside-middle.png
Sending file modes: C0664 763096 IUPS_white.png
Sink: C0664 763096 IUPS_white.png
Sending file modes: C0664 257339 Run_button.svg
Sink: C0664 257339 Run_button.svg
Sending file modes: C0664 420195 Horizonal_Online.png
Sink: C0664 420195 Horizonal_Online.png
Sending file modes: C0664 257344 Fulltext_button.svg
Sink: C0664 257344 Fulltext_button.svg
Sending file modes: C0664 407504 ABI_Positive_RGB.jpg
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 1 clearing O_NONBLOCK
debug1: fd 2 clearing O_NONBLOCK
Transferred: sent 24486916, received 46372 bytes, in 1.2 seconds
Bytes per second: sent 19609093.7, received 37134.6
debug1: Exit status 0
Finished: SUCCESS