Started by GitHub push by nickerso
Running as SYSTEM
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/* # 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
> 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/* # timeout=10
> git rev-parse refs/remotes/origin/journaldev^{commit} # timeout=10
> git rev-parse refs/remotes/origin/origin/journaldev^{commit} # timeout=10
Checking out Revision 3e3b37345a20956966a44ccbbbe762bb44866f7d (refs/remotes/origin/journaldev)
> git config core.sparsecheckout # timeout=10
> git checkout -f 3e3b37345a20956966a44ccbbbe762bb44866f7d # timeout=10
Commit message: "Merge pull request #38 from KarinLundengard/TemporaryStagingForIUPS"
> git rev-list --no-walk 28a6146accfe990b9eb0527a2e1919db8b5c9920 # timeout=10
[Set GitHub commit status (universal)] PENDING on repos [GHRepository@19e6c9c0[description=Source for journal.physiomeproject.org.,homepage=<null>,name=journal-website,fork=false,archived=false,size=14858,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=[Tue, 04 Feb 2020 11:24:22 GMT], ETag=[W/"82e5d7a1e45810ce4c537b222d48aea3"], Last-Modified=[Tue, 04 Feb 2020 11:24:02 GMT], OkHttp-Received-Millis=[1580815462255], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1580815461838], 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=[A57C:080E:1DECC8:22C54C:5E395465], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4999], X-RateLimit-Reset=[1580819062], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/Physiome/journal-website,id=94735176]] (sha:3e3b373) with context:journaldev-build
Setting commit status on GitHub for https://github.com/Physiome/journal-website/commit/3e3b37345a20956966a44ccbbbe762bb44866f7d
[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/shiningpanda16715300211467004558.sh
+ make deps
pip install -r py-requirements.txt
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Collecting pelican>3.6
Using cached pelican-4.2.0-py2.py3-none-any.whl (258 kB)
Collecting markdown
Using cached Markdown-3.1.1-py2.py3-none-any.whl (87 kB)
Collecting six>=1.4
Using cached six-1.14.0-py2.py3-none-any.whl (10 kB)
Processing /home/cmiss/.cache/pip/wheels/ac/c9/63/61e224fe1b2442b36e18f2e1c13b97fa4ce3ba7211d92f9401/feedgenerator-1.9-cp27-none-any.whl
Processing /home/cmiss/.cache/pip/wheels/92/a0/00/8690a57883956a301d91cf4ec999cc0b258b01e3f548f86e89/blinker-1.4-cp27-none-any.whl
Collecting unidecode
Using cached Unidecode-1.1.1-py2.py3-none-any.whl (238 kB)
Collecting python-dateutil
Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pytz>=0a
Using cached pytz-2019.3-py2.py3-none-any.whl (509 kB)
Collecting docutils
Using cached docutils-0.16-py2.py3-none-any.whl (548 kB)
Collecting jinja2>=2.7
Downloading Jinja2-2.11.1-py2.py3-none-any.whl (126 kB)
Collecting pygments
Using cached Pygments-2.5.2-py2.py3-none-any.whl (896 kB)
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)) (44.0.0)
Collecting MarkupSafe>=0.23
Using cached MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl (24 kB)
Installing collected packages: six, pytz, feedgenerator, blinker, unidecode, python-dateutil, docutils, MarkupSafe, jinja2, pygments, pelican, markdown
Successfully installed MarkupSafe-1.1.1 blinker-1.4 docutils-0.16 feedgenerator-1.9 jinja2-2.11.1 markdown-3.1.1 pelican-4.2.0 pygments-2.5.2 python-dateutil-2.8.1 pytz-2019.3 six-1.14.0 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 2 articles, 0 drafts, 6 pages, 0 hidden pages and 0 draft pages in 0.55 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 7386 about.html
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Entering directory: D0775 0 archive-descriptions
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Sink: E
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Entering directory: D0775 0 articles
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Sending file modes: C0664 6492 incorporation-of-sarcolemmal-calcium-transporters-into-the-shorten-et-al-2007-model-of-skeletal-muscle-equations-coding-and-stability.html
Sink: C0664 6492 incorporation-of-sarcolemmal-calcium-transporters-into-the-shorten-et-al-2007-model-of-skeletal-muscle-equations-coding-and-stability.html
Sending file modes: C0664 6674 the-cardiac-nak-atpase-an-updated-thermodynamically-consistent-model.html
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Sending file modes: C0664 6384 index.html
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Sending file modes: C0664 4438 articles.html
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Entering directory: D0775 0 author
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Sending file modes: C0664 8947 the-physiome-project.html
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Sink: E
Sending file modes: C0664 3862 authors.html
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Sending file modes: C0664 3862 categories.html
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Entering directory: D0775 0 data
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Sending file modes: C0664 625571 nickerson-and-noble-1962.csv
Sink: C0664 625571 nickerson-and-noble-1962.csv
Sink: E
Sending file modes: C0664 5022 editorial-board.html
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Sending file modes: C0664 8947 index.html
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Sending file modes: C0664 17387 instructions-to-authors.html
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Entering directory: D0775 0 models
Sink: D0775 0 models
Entering directory: D0775 0 ccm
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Sending file modes: C0664 449150 nerves_2.json
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Sending file modes: C0664 3156133 jaw_2.json
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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 6453 physiome-project.html
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Sending file modes: C0664 4245 pmr.html
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Entering directory: D0775 0 theme
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Entering directory: D0775 0 models
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debug1: channel 0: free: client-session, nchannels 1
debug1: fd 0 clearing O_NONBLOCK
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Transferred: sent 22748184, received 42888 bytes, in 2.6 seconds
Bytes per second: sent 8781079.1, received 16555.3
debug1: Exit status 0
[Set GitHub commit status (universal)] SUCCESS on repos [GHRepository@7e9a4482[description=Source for journal.physiomeproject.org.,homepage=<null>,name=journal-website,fork=false,archived=false,size=14858,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=[Tue, 04 Feb 2020 11:24:22 GMT], ETag=[W/"82e5d7a1e45810ce4c537b222d48aea3"], Last-Modified=[Tue, 04 Feb 2020 11:24:02 GMT], OkHttp-Received-Millis=[1580815462255], OkHttp-Response-Source=[CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1580815461838], 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=[A57C:080E:1DECC8:22C54C:5E395465], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4999], X-RateLimit-Reset=[1580819062], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/Physiome/journal-website,id=94735176]] (sha:3e3b373) with context:journaldev-build
Setting commit status on GitHub for https://github.com/Physiome/journal-website/commit/3e3b37345a20956966a44ccbbbe762bb44866f7d
Finished: SUCCESS