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Started by GitHub push by KarinLundengard 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 c74d9d7e171be0ca3e203a96d769ae1bcf1bfa0f (refs/remotes/origin/journaldev) > git config core.sparsecheckout # timeout=10 > git checkout -f c74d9d7e171be0ca3e203a96d769ae1bcf1bfa0f # timeout=10 Commit message: "Merge pull request #58 from KarinLundengard/TemporaryStagingForIUPS" > git rev-list --no-walk 5331f6d0316160f90460acd1bdc7381a7b0f80fa # timeout=10 [Set GitHub commit status (universal)] PENDING on repos [GHRepository@6eed0a16[description=Source for journal.physiomeproject.org.,homepage=<null>,name=journal-website,fork=false,archived=false,size=16438,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, Deprecation, Sunset], 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=[Thu, 18 Jun 2020 23:05:50 GMT], ETag=[W/"1864dfc727310ce584b0a10f7f96c6cb"], Last-Modified=[Thu, 18 Jun 2020 23:05:32 GMT], OkHttp-Received-Millis=[1592521550075], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1592521549714], 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, Accept, X-Requested-With, 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=[9338:01BC:C3D39:E27E4:5EEBF34D], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4999], X-RateLimit-Reset=[1592525149], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/Physiome/journal-website,id=94735176]] (sha:c74d9d7) with context:journaldev-build Setting commit status on GitHub for https://github.com/Physiome/journal-website/commit/c74d9d7e171be0ca3e203a96d769ae1bcf1bfa0f [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/shiningpanda5634342448630473255.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. pip 21.0 will drop support for Python 2.7 in January 2021. 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-1.15.0-py2.py3-none-any.whl (10 kB) Processing /home/cmiss/.cache/pip/wheels/68/1c/e0/44629d259095aa5f4af96d3c4638f46998e4c5b9b02c1cad3f/feedgenerator-1.9.1-py2-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-2020.1-py2.py3-none-any.whl (510 kB) Collecting docutils Using cached docutils-0.16-py2.py3-none-any.whl (548 kB) Collecting jinja2>=2.7 Using cached Jinja2-2.11.2-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)) (44.1.1) 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-1.9.1 jinja2-2.11.2 markdown-3.1.1 pelican-4.2.0 pygments-2.5.2 python-dateutil-2.8.1 pytz-2020.1 six-1.15.0 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 3 articles, 0 drafts, 7 pages, 0 hidden pages and 0 draft pages in 0.81 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/testing.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 12410 about.html Sink: C0664 12410 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 3874 archives.html Sink: C0664 3874 archives.html Entering directory: D0775 0 articles Sink: D0775 0 articles Entering directory: D0775 0 10.5072 Sink: D0775 0 10.5072 Sending file modes: C0664 6762 FK2.stagefigshare.6853437.html Sink: C0664 6762 FK2.stagefigshare.6853437.html 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index.html Sink: C0664 10082 index.html Sending file modes: C0664 22362 instructions-to-authors.html Sink: C0664 22362 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: C0664 4891 physiome-project.html Sink: C0664 4891 physiome-project.html Sending file modes: C0664 4257 pmr.html Sink: C0664 4257 pmr.html Sending file modes: C0664 3874 tags.html Sink: C0664 3874 tags.html Sending file modes: C0664 3976 testing.html Sink: C0664 3976 testing.html Entering directory: D0775 0 theme Sink: D0775 0 theme Entering directory: D0775 0 js Sink: D0775 0 js Sending file modes: C0664 257551 jquery.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 Sink: D0775 0 models Sending file modes: C0664 524257 three.min.js 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 Sink: E Sending file modes: C0664 123510 foundation.min.js Sink: C0664 123510 foundation.min.js Sending file modes: C0664 333138 foundation.js Sink: C0664 333138 foundation.js Entering directory: D0775 0 views Sink: D0775 0 views Sending file modes: C0664 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