Started by GitHub push by nickerso
Running as SYSTEM
Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/PhysiomeJournalSite
The recommended git tool is: NONE
No credentials specified
> git rev-parse --resolve-git-dir /home/cmiss/Jenkins/workspace/PhysiomeJournalSite/.git # 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 2.25.1'
> git fetch --tags --force --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 6b96141ba326c83b6cf8050ad2d50ac49a6a6388 (refs/remotes/origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f 6b96141ba326c83b6cf8050ad2d50ac49a6a6388 # timeout=10
Commit message: "Merge pull request #191 from Physiome/journaldev"
> git rev-list --no-walk 2add74ddfd271a4e54bc895c2fbf6214608376af # timeout=10
[PhysiomeJournalSite] $ /bin/sh -xe /tmp/shiningpanda8420088335550214040.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)) (4.8.0)
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)) (3.4.1)
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)) (3.1.2)
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)) (0.19)
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)) (1.5)
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)) (2.0.0)
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)) (2.8.2)
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)) (2.14.0)
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)) (2022.7.1)
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)) (1.3.6)
Requirement already satisfied: rich>=10.1 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (13.2.0)
Requirement already satisfied: importlib-metadata>=4.4 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from markdown->-r py-requirements.txt (line 2)) (6.0.0)
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>=4.4->markdown->-r py-requirements.txt (line 2)) (4.4.0)
Requirement already satisfied: zipp>=0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from importlib-metadata>=4.4->markdown->-r py-requirements.txt (line 2)) (3.11.0)
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)) (2.1.2)
Requirement already satisfied: six>=1.5 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from python-dateutil>=2.8->pelican>3.6->-r py-requirements.txt (line 1)) (1.16.0)
Requirement already satisfied: markdown-it-py<3.0.0,>=2.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from rich>=10.1->pelican>3.6->-r py-requirements.txt (line 1)) (2.1.0)
Requirement already satisfied: mdurl~=0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from markdown-it-py<3.0.0,>=2.1.0->rich>=10.1->pelican>3.6->-r py-requirements.txt (line 1)) (0.1.2)
+ 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 16 articles, 0 drafts, 0 hidden articles, 9 pages, 0 hidden
pages and 0 draft pages in 0.58 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/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_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/journal.physiomeproject.org/
Sending file modes: C0664 19801 about.html
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Entering directory: D0775 0 archive-descriptions
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Sending file modes: C0664 9621 archives.html
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Entering directory: D0775 0 articles
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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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Sink: E
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Entering directory: D0775 0 author
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Sending file modes: C0664 19518 the-physiome-project.html
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Entering directory: D0775 0 data
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Entering directory: D0775 0 models
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Entering directory: D0775 0 ccm
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Sink: E
Sink: E
Entering directory: D0775 0 pdfs
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Sending file modes: C0664 772737 A model of pH control v4.pdf
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Sink: E
Sending file modes: C0664 10817 physiome-project.html
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Sending file modes: C0664 10160 pmr.html
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Entering directory: D0775 0 theme
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Entering directory: D0775 0 models
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Entering directory: D0775 0 css
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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 2 clearing O_NONBLOCK
Transferred: sent 24758460, received 45756 bytes, in 1.1 seconds
Bytes per second: sent 22377471.2, received 41355.7
debug1: Exit status 0
Finished: SUCCESS