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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 d0cb66b8475051239cdcd231f6bbd582c82faf8f (refs/remotes/origin/journaldev) > git config core.sparsecheckout # timeout=10 > git checkout -f d0cb66b8475051239cdcd231f6bbd582c82faf8f Commit message: "Merge pull request #9 from KarinLundengard/AddArticles" > git rev-list --no-walk 8cd2857e81b2b81a590a2bc909a5a2fea56d65d2 # timeout=10 [Set GitHub commit status (universal)] PENDING on repos [GHRepository@74ed3384[description=Source for journal.physiomeproject.org.,homepage=<null>,name=journal-website,fork=false,archived=false,size=13904,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=[Mon, 10 Jun 2019 04:03:10 GMT], ETag=[W/"240115532c4c6ca74705d7475e6ea4e4"], Last-Modified=[Mon, 10 Jun 2019 04:02:53 GMT], OkHttp-Received-Millis=[1560139390442], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1560139390136], 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=[EE16:3007:19D4F2:1FFDD3:5CFDD67D], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4999], X-RateLimit-Reset=[1560142990], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/Physiome/journal-website,id=94735176]] (sha:d0cb66b) with context:journaldev-build Setting commit status on GitHub for https://github.com/Physiome/journal-website/commit/d0cb66b8475051239cdcd231f6bbd582c82faf8f [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/shiningpanda4999453719249753386.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/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/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/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 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)) Downloading https://files.pythonhosted.org/packages/5c/73/1dfa428150e3ccb0fa3e68db406e5be48698f2a979ccbcec795f28f44048/Pygments-2.4.2-py2.py3-none-any.whl (883kB) 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 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 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, pygments, blinker, docutils, python-dateutil, 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-4.0.1 pygments-2.4.2 python-dateutil-2.8.0 pytz-2019.1 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 9 articles, 0 drafts, 6 pages, 0 hidden pages and 0 draft pages in 0.29 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 5961 about.html Sink: C0664 5961 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 Sink: E Sending file modes: C0664 2393 archives.html Sink: C0664 2393 archives.html Entering directory: D0775 0 articles Sink: D0775 0 articles Sending file modes: C0664 2598 ph-regulation.html Sink: C0664 2598 ph-regulation.html Entering directory: D0775 0 10.6084 Sink: D0775 0 10.6084 Sending file modes: C0664 4757 m9.figshare.c.3841336.html Sink: C0664 4757 m9.figshare.c.3841336.html Sink: E Sending file modes: C0664 3963 cerebral-circulation-model.html Sink: C0664 3963 cerebral-circulation-model.html Sending file modes: C0664 2659 cerebal-circulation-model.html Sink: C0664 2659 cerebal-circulation-model.html Sending file modes: C0664 2887 noble-62-model.html Sink: C0664 2887 noble-62-model.html Sending file modes: C0664 2805 denis-noble-skeletal-muscle-modelling.html Sink: C0664 2805 denis-noble-skeletal-muscle-modelling.html Sending file modes: C0664 2643 thermodynamically-consistent-model-of-the-cardiac-nak-atpase.html Sink: C0664 2643 thermodynamically-consistent-model-of-the-cardiac-nak-atpase.html Entering directory: D0775 0 10.5072 Sink: D0775 0 10.5072 Sending file modes: C0664 5393 FK2.stagefigshare.c.2732114.v3.html Sink: C0664 5393 FK2.stagefigshare.c.2732114.v3.html Sink: E Sending file modes: C0664 6471 index.html Sink: C0664 6471 index.html Sending file modes: C0664 2804 force-dependent-affinity-of-troponin-for-ca2-explains-the-difference-between-the-isotonic-and-isometric-cardiac-end-systolic-force-length-relations.html Sink: C0664 2804 force-dependent-affinity-of-troponin-for-ca2-explains-the-difference-between-the-isotonic-and-isometric-cardiac-end-systolic-force-length-relations.html Sink: E Sending file modes: C0664 2969 articles.html Sink: C0664 2969 articles.html Entering directory: D0775 0 author Sink: D0775 0 author Sending file modes: C0664 8769 the-physiome-project.html Sink: C0664 8769 the-physiome-project.html Sink: E Sending file modes: C0664 2393 authors.html Sink: C0664 2393 authors.html Sending file modes: C0664 2393 categories.html Sink: C0664 2393 categories.html Entering directory: D0775 0 data Sink: D0775 0 data Sending file modes: C0664 625571 nickerson-and-noble-1962.csv Sink: C0664 625571 nickerson-and-noble-1962.csv Sending file modes: C0664 3363 editorial-board.html Sink: E Sink: C0664 3363 editorial-board.html Sending file modes: C0664 8769 index.html Sink: C0664 8769 index.html Sending file modes: C0664 15896 instructions-to-authors.html Sink: C0664 15896 instructions-to-authors.html Entering directory: D0775 0 models Entering directory: D0775 0 ccm Sink: D0775 0 models Sending file modes: C0664 449150 nerves_2.json Sink: D0775 0 ccm Sink: C0664 449150 nerves_2.json Sending file modes: C0664 201 jaw_1.json Sink: C0664 201 jaw_1.json Sending file modes: C0664 161 jaw_view.json Sink: C0664 161 jaw_view.json Sending file modes: C0664 174 nerves_1.json Sink: C0664 174 nerves_1.json Sending file modes: C0664 3156133 jaw_2.json Sink: C0664 3156133 jaw_2.json Sink: E Entering directory: D0775 0 pdfs Sink: E Sending file modes: C0664 772737 A model of pH control v4.pdf Sink: D0775 0 pdfs Sink: C0664 772737 A model of pH control v4.pdf Sending file modes: C0664 4984 physiome-project.html Sink: E Sink: C0664 4984 physiome-project.html Sending file modes: C0664 2776 pmr.html Sink: C0664 2776 pmr.html Sending file modes: C0664 2393 tags.html Sink: C0664 2393 tags.html Entering directory: D0775 0 theme Entering directory: D0775 0 js Sink: D0775 0 theme Sending file modes: C0664 257551 jquery.js Sink: D0775 0 js Sink: C0664 257551 jquery.js Sending file modes: C0664 0 andre.js Sink: C0664 0 andre.js Sending file modes: C0664 8663 what-input.js Sink: C0664 8663 what-input.js Entering directory: D0775 0 models Sending file modes: C0664 524257 three.min.js Sink: D0775 0 models Sink: C0664 524257 three.min.js Sending file modes: C0664 48448 zinc_3js_renderer.js Sink: C0664 48448 zinc_3js_renderer.js Sending file modes: C0664 35330 zinc_threejs_control.js Sink: C0664 35330 zinc_threejs_control.js Sending file modes: C0664 123510 foundation.min.js Sink: E Sink: C0664 123510 foundation.min.js Sending file modes: C0664 333138 foundation.js Sink: C0664 333138 foundation.js Entering directory: D0775 0 views Sending file modes: C0664 1928 cellml.js Sink: D0775 0 views Sink: C0664 1928 cellml.js Sending file 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