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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 328b82b40a9f269e45938d66108abcdd3966546a (refs/remotes/origin/journaldev) > git config core.sparsecheckout # timeout=10 > git checkout -f 328b82b40a9f269e45938d66108abcdd3966546a # timeout=10 Commit message: "Merge pull request #34 from KarinLundengard/journaldev" > git rev-list --no-walk ae0760efaa035859cdf0f9c5906e1033d634a6a7 # timeout=10 [Set GitHub commit status (universal)] PENDING on repos [GHRepository@7460f9fd[description=Source for journal.physiomeproject.org.,homepage=<null>,name=journal-website,fork=false,archived=false,size=14848,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, 27 Jan 2020 05:31:35 GMT], ETag=[W/"91b89cd74129a6d2803e59c36d8fc920"], Last-Modified=[Mon, 27 Jan 2020 05:31:15 GMT], OkHttp-Received-Millis=[1580103095261], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1580103094881], 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=[DE14:1D00:500C3D:5C15BE:5E2E75B6], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4998], X-RateLimit-Reset=[1580106695], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/Physiome/journal-website,id=94735176]] (sha:328b82b) with context:journaldev-build Setting commit status on GitHub for https://github.com/Physiome/journal-website/commit/328b82b40a9f269e45938d66108abcdd3966546a [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/shiningpanda17751723200604417204.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 Downloading 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 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Collecting jinja2>=2.7 Using cached Jinja2-2.10.3-py2.py3-none-any.whl (125 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 jinja2-2.10.3 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 8 articles, 0 drafts, 6 pages, 0 hidden pages and 0 draft pages in 0.65 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 Sink: C0664 7386 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 3862 archives.html Sink: C0664 3862 archives.html Entering directory: D0775 0 articles Sink: D0775 0 articles Sending file modes: C0664 5108 incorporation-of-sarcolemmal-calcium-transporters-into-the-shorten-et-al-2007-model-of-skeletal-muscle-equations-coding-and-stability.html Sink: 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FK2.stagefigshare.c.2732114.v3.html Sink: E Sending file modes: C0664 8107 index.html Sink: C0664 8107 index.html Sending file modes: C0664 4470 force-dependent-affinity-of-troponin-for-ca2-explains-the-difference-between-the-isotonic-and-isometric-cardiac-end-systolic-force-length-relations.html Sink: C0664 4470 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 4438 articles.html Sink: C0664 4438 articles.html Entering directory: D0775 0 author Sink: D0775 0 author Sending file modes: C0664 6024 the-physiome-project.html Sink: C0664 6024 the-physiome-project.html Sink: E Sending file modes: C0664 3862 authors.html Sink: C0664 3862 authors.html Sending file modes: C0664 3862 categories.html Sink: C0664 3862 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 Sink: E Sending file modes: C0664 5022 editorial-board.html Sink: C0664 5022 editorial-board.html Sending file modes: C0664 6024 index.html Sink: C0664 6024 index.html Sending file modes: C0664 17387 instructions-to-authors.html Sink: C0664 17387 instructions-to-authors.html Entering directory: D0775 0 models Sink: D0775 0 models Entering directory: D0775 0 ccm Sink: D0775 0 ccm Sending file modes: C0664 449150 nerves_2.json 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 Sink: E Entering directory: D0775 0 pdfs Sink: D0775 0 pdfs 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: 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