Started by GitHub push by nickerso
Building remotely on Ubuntu_16.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite
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 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/*
 > git rev-parse refs/remotes/origin/journaldev^{commit} # timeout=10
 > git rev-parse refs/remotes/origin/origin/journaldev^{commit} # timeout=10
Checking out Revision a0962bbd2d0ee77543c2abbe873c963534c32b31 (refs/remotes/origin/journaldev)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f a0962bbd2d0ee77543c2abbe873c963534c32b31
Commit message: "Merge pull request #29 from KarinLundengard/FooterAndCOMBINEuppdates"
 > git rev-list --no-walk 3f6b050e2c02a92ba7993a0355ae6a89eb83ec3d # timeout=10
[Set GitHub commit status (universal)] PENDING on repos [GHRepository@4268e499[description=Source for journal.physiomeproject.org.,homepage=<null>,name=journal-website,fork=false,archived=false,size=14403,milestones={},language=HTML,commits={},source=<null>,parent=<null>,responseHeaderFields={null=[HTTP/1.1 200 OK], Access-Control-Allow-Origin=[*], Access-Control-Expose-Headers=[ETag, Link, Location, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval, X-GitHub-Media-Type], Cache-Control=[private, max-age=60, s-maxage=60], Content-Encoding=[gzip], Content-Security-Policy=[default-src 'none'], Content-Type=[application/json; charset=utf-8], Date=[Fri, 19 Jul 2019 20:33:46 GMT], ETag=[W/"2646c1f2bfa2e496236a555f7a1e834f"], Last-Modified=[Fri, 19 Jul 2019 20:33:29 GMT], OkHttp-Received-Millis=[1563568426128], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1563568425824], Referrer-Policy=[origin-when-cross-origin, strict-origin-when-cross-origin], Server=[GitHub.com], Status=[200 OK], Strict-Transport-Security=[max-age=31536000; includeSubdomains; preload], Transfer-Encoding=[chunked], Vary=[Accept, Authorization, Cookie, X-GitHub-OTP, Accept-Encoding], X-Accepted-OAuth-Scopes=[repo], X-Content-Type-Options=[nosniff], X-Frame-Options=[deny], X-GitHub-Media-Type=[github.v3; format=json], X-GitHub-Request-Id=[E220:8DA9:1B49D90:20E99DB:5D322929], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4999], X-RateLimit-Reset=[1563572026], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/Physiome/journal-website,id=94735176]] (sha:a0962bb) with context:journaldev-build
Setting commit status on GitHub for https://github.com/Physiome/journal-website/commit/a0962bbd2d0ee77543c2abbe873c963534c32b31
[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/shiningpanda15225021220768464603.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/ba/38/9969a46cf0e15b14858e48f4933cc89baf5fb51cf6160a86e65435bc8dbb/pelican-4.1.0-py2.py3-none-any.whl
Collecting markdown (from -r py-requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/c0/4e/fd492e91abdc2d2fcb70ef453064d980688762079397f779758e055f6575/Markdown-3.1.1-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/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl
Collecting unidecode (from pelican>3.6->-r py-requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/d0/42/d9edfed04228bacea2d824904cae367ee9efd05e6cce7ceaaedd0b0ad964/Unidecode-1.1.1-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/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-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 pygments (from pelican>3.6->-r py-requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/5c/73/1dfa428150e3ccb0fa3e68db406e5be48698f2a979ccbcec795f28f44048/Pygments-2.4.2-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 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
Requirement already satisfied: setuptools>=36 in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/lib/python2.7/site-packages (from markdown->-r py-requirements.txt (line 2)) (41.0.1)
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, feedgenerator, python-dateutil, pygments, blinker, docutils, pelican, markdown
Successfully installed MarkupSafe-1.1.1 blinker-1.4 docutils-0.14 feedgenerator-1.9 jinja2-2.10.1 markdown-3.1.1 pelican-4.1.0 pygments-2.4.2 python-dateutil-2.8.0 pytz-2019.1 six-1.12.0 unidecode-1.1.1
+ make html
pelican /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite/content -o /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite/output -s /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite/pelicanconf.py 
WARNING: Replacement Indicator '{SITEURL' not recognized, skipping replacement
Done: Processed 8 articles, 0 drafts, 6 pages, 0 hidden pages and 0 draft pages in 0.57 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/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-4ubuntu0.3, 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 [130.216.4.34] 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: Local version string SSH-2.0-OpenSSH_7.6p1 Ubuntu-4ubuntu0.3
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 7222 about.html
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Entering directory: D0775 0 archive-descriptions
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Entering directory: D0775 0 author
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Sending file modes: C0664 10362 the-physiome-project.html
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Entering directory: D0775 0 models
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Entering directory: D0775 0 ccm
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debug1: fd 0 clearing O_NONBLOCK
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debug1: fd 2 clearing O_NONBLOCK
Transferred: sent 22779472, received 43868 bytes, in 2.0 seconds
Bytes per second: sent 11133455.5, received 21440.5
debug1: Exit status 0
[Set GitHub commit status (universal)] SUCCESS on repos [GHRepository@1f75fa30[description=Source for journal.physiomeproject.org.,homepage=<null>,name=journal-website,fork=false,archived=false,size=14403,milestones={},language=HTML,commits={},source=<null>,parent=<null>,responseHeaderFields={null=[HTTP/1.1 200 OK], Access-Control-Allow-Origin=[*], Access-Control-Expose-Headers=[ETag, Link, Location, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval, X-GitHub-Media-Type], Cache-Control=[private, max-age=60, s-maxage=60], Content-Encoding=[gzip], Content-Security-Policy=[default-src 'none'], Content-Type=[application/json; charset=utf-8], Date=[Fri, 19 Jul 2019 20:33:46 GMT], ETag=[W/"2646c1f2bfa2e496236a555f7a1e834f"], Last-Modified=[Fri, 19 Jul 2019 20:33:29 GMT], OkHttp-Received-Millis=[1563568426128], OkHttp-Response-Source=[CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1563568425824], Referrer-Policy=[origin-when-cross-origin, strict-origin-when-cross-origin], Server=[GitHub.com], Status=[200 OK], Strict-Transport-Security=[max-age=31536000; includeSubdomains; preload], Transfer-Encoding=[chunked], Vary=[Accept, Authorization, Cookie, X-GitHub-OTP, Accept-Encoding], X-Accepted-OAuth-Scopes=[repo], X-Content-Type-Options=[nosniff], X-Frame-Options=[deny], X-GitHub-Media-Type=[github.v3; format=json], X-GitHub-Request-Id=[E220:8DA9:1B49D90:20E99DB:5D322929], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4999], X-RateLimit-Reset=[1563572026], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/Physiome/journal-website,id=94735176]] (sha:a0962bb) with context:journaldev-build
Setting commit status on GitHub for https://github.com/Physiome/journal-website/commit/a0962bbd2d0ee77543c2abbe873c963534c32b31
Finished: SUCCESS