GitHub pull request #3 of commit 46c567114492e4bae86bf2b5958079ccbd46b80f, no merge conflicts.
Setting status of 46c567114492e4bae86bf2b5958079ccbd46b80f to PENDING with url http://autotest.bioeng.auckland.ac.nz/jenkins/job/PhysiomeJournalDevelopmentSite/4/ and message: 'Build started for merge commit.'
Using context: journaldev
Setting status of 46c567114492e4bae86bf2b5958079ccbd46b80f to PENDING with url http://autotest.bioeng.auckland.ac.nz/jenkins/job/PhysiomeJournalDevelopmentSite/4/ and message: 'Build started for merge commit.'
Using context: journaldev
Building remotely on Ubuntu_16.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite
[WS-CLEANUP] Deleting project workspace...
[WS-CLEANUP] Deferred wipeout is used...
[WS-CLEANUP] Done
No credentials specified
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 fetch --tags --progress https://github.com/Physiome/journal-website +refs/heads/*:refs/remotes/origin/*
> 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
> git config remote.origin.url https://github.com/Physiome/journal-website # timeout=10
Fetching upstream changes from https://github.com/Physiome/journal-website
> git fetch --tags --progress https://github.com/Physiome/journal-website +refs/heads/*:refs/remotes/origin/*
Seen branch in repository origin/journaldev
Seen branch in repository origin/master
Seen 2 remote branches
> git show-ref --tags -d # timeout=10
Checking out Revision 3adbd36839acb0b60f04e002ca5e0ab7b886cbc5 (origin/journaldev, origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f 3adbd36839acb0b60f04e002ca5e0ab7b886cbc5
Commit message: "One more Jenkins test"
First time build. Skipping changelog.
[PhysiomeJournalDevelopmentSite] $ /usr/bin/python2.7 /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9
New python executable in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/bin/python2.7
Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/bin/python
Installing setuptools, pip, wheel...done.
[PhysiomeJournalDevelopmentSite] $ /bin/sh -xe /tmp/shiningpanda8331570865262402653.sh
+ make deps
pip install -r py-requirements.txt
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.
Collecting pelican>3.6 (from -r py-requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/a4/80/0a474a4aa30fab1666f63c2118d89bcbc05dc3180d791ab90d5e90b7f2e0/pelican-4.0.1-py2.py3-none-any.whl
Collecting markdown (from -r py-requirements.txt (line 2))
Using cached https://files.pythonhosted.org/packages/7a/6b/5600647404ba15545ec37d2f7f58844d690baf2f81f3a60b862e48f29287/Markdown-3.0.1-py2.py3-none-any.whl
Collecting pytz>=0a (from pelican>3.6->-r py-requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl
Collecting unidecode (from pelican>3.6->-r py-requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/31/39/53096f9217b057cb049fe872b7fc7ce799a1a89b76cf917d9639e7a558b5/Unidecode-1.0.23-py2.py3-none-any.whl
Collecting jinja2>=2.7 (from pelican>3.6->-r py-requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl
Collecting six>=1.4 (from pelican>3.6->-r py-requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pygments (from pelican>3.6->-r py-requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl
Collecting blinker (from pelican>3.6->-r py-requirements.txt (line 1))
Collecting docutils (from pelican>3.6->-r py-requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/50/09/c53398e0005b11f7ffb27b7aa720c617aba53be4fb4f4f3f06b9b5c60f28/docutils-0.14-py2-none-any.whl
Collecting feedgenerator>=1.9 (from pelican>3.6->-r py-requirements.txt (line 1))
Collecting python-dateutil (from pelican>3.6->-r py-requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from jinja2>=2.7->pelican>3.6->-r py-requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/fb/40/f3adb7cf24a8012813c5edb20329eb22d5d8e2a0ecf73d21d6b85865da11/MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl
Installing collected packages: pytz, unidecode, MarkupSafe, jinja2, six, pygments, blinker, docutils, feedgenerator, python-dateutil, pelican, markdown
Successfully installed MarkupSafe-1.1.1 blinker-1.4 docutils-0.14 feedgenerator-1.9 jinja2-2.10 markdown-3.0.1 pelican-4.0.1 pygments-2.3.1 python-dateutil-2.8.0 pytz-2018.9 six-1.12.0 unidecode-1.0.23
+ 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 3 articles, 0 drafts, 5 pages, 0 hidden pages and 0 draft pages in 0.24 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/tags.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_7.2p2 Ubuntu-4ubuntu2.8, OpenSSL 1.0.2g 1 Mar 2016
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 [130.216.4.34] 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: Enabling compatibility mode for protocol 2.0
debug1: Local version string SSH-2.0-OpenSSH_7.2p2 Ubuntu-4ubuntu2.8
debug1: Remote protocol version 2.0, remote software version OpenSSH_7.2p2 Ubuntu-4ubuntu2.8
debug1: match: OpenSSH_7.2p2 Ubuntu-4ubuntu2.8 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@libssh.org
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=<rsa-sha2-256,rsa-sha2-512>
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 ([130.216.4.34]: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/journaldev.physiomeproject.org/
Sending file modes: C0664 6221 about.html
Sink: C0664 6221 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
Sending file modes: C0664 2720 archives.html
Sink: E
Sink: C0664 2720 archives.html
Entering directory: D0775 0 articles
Entering directory: D0775 0 10.6084
Sink: D0775 0 articles
Sending file modes: C0664 4547 m9.figshare.c.3841336.html
Sink: D0775 0 10.6084
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Sink: E
Sending file modes: C0664 4285 cerebral-circulation-model.html
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Entering directory: D0775 0 10.5072
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Sink: E
Sending file modes: C0664 4502 index.html
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Sending file modes: C0664 3296 articles.html
Sink: E
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Entering directory: D0775 0 author
Sending file modes: C0664 6055 the-physiome-project.html
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Sending file modes: C0664 2720 authors.html
Sink: E
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Sending file modes: C0664 2720 categories.html
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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 3690 editorial-board.html
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Sending file modes: C0664 6055 index.html
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Sending file modes: C0664 6505 instructions-to-authors.html
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Entering directory: D0775 0 models
Entering directory: D0775 0 ccm
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Sending file modes: C0664 449150 nerves_2.json
Sink: D0775 0 ccm
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Sending file modes: C0664 201 jaw_1.json
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Sending file modes: C0664 161 jaw_view.json
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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
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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 5311 physiome-project.html
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Sending file modes: C0664 2720 tags.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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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 8552328, received 39168 bytes, in 1.5 seconds
Bytes per second: sent 5708417.8, received 26143.4
debug1: Exit status 0
Setting status of 46c567114492e4bae86bf2b5958079ccbd46b80f to SUCCESS with url http://autotest.bioeng.auckland.ac.nz/jenkins/job/PhysiomeJournalDevelopmentSite/4/ and message: 'Build finished. '
Using context: journaldev
Setting status of 46c567114492e4bae86bf2b5958079ccbd46b80f to SUCCESS with url http://autotest.bioeng.auckland.ac.nz/jenkins/job/PhysiomeJournalDevelopmentSite/4/ and message: ' '
Using context: journaldev
Finished: SUCCESS