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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/PhysiomeJournalSite The recommended git tool is: NONE No credentials specified > git rev-parse --is-inside-work-tree # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/Physiome/journal-website # timeout=10 Fetching upstream changes from https://github.com/Physiome/journal-website > git --version # timeout=10 > git --version # 'git version 2.17.1' > git fetch --tags --progress -- https://github.com/Physiome/journal-website +refs/heads/*:refs/remotes/origin/* # timeout=10 > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 > git rev-parse refs/remotes/origin/origin/master^{commit} # timeout=10 Checking out Revision f2a3d4244f5efdbc135b8e8ff3643698c82813fd (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f f2a3d4244f5efdbc135b8e8ff3643698c82813fd # timeout=10 Commit message: "Merge pull request #95 from Physiome/journaldev" > git rev-list --no-walk 6daa44440a9c2912bcfe6a58a81c8f3942d18254 # timeout=10 [PhysiomeJournalSite] $ /bin/sh -xe /tmp/shiningpanda460011621395618756.sh + make deps pip install -r py-requirements.txt Requirement already satisfied: pelican>3.6 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from -r py-requirements.txt (line 1)) (4.5.0) Requirement already satisfied: markdown in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from -r py-requirements.txt (line 2)) (3.2.2) Requirement already satisfied: python-dateutil in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (2.8.1) Requirement already satisfied: blinker in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (1.4) Requirement already satisfied: feedgenerator>=1.9 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (1.9.1) Requirement already satisfied: pytz>=0a in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (2020.1) Requirement already satisfied: unidecode in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (1.1.1) Requirement already satisfied: docutils>=0.15 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (0.16) Requirement already satisfied: pygments in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (2.6.1) Requirement already satisfied: jinja2>=2.11 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (2.11.2) Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from markdown->-r py-requirements.txt (line 2)) (1.7.0) Requirement already satisfied: six>=1.5 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from python-dateutil->pelican>3.6->-r py-requirements.txt (line 1)) (1.15.0) Requirement already satisfied: MarkupSafe>=0.23 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from jinja2>=2.11->pelican>3.6->-r py-requirements.txt (line 1)) (1.1.1) Requirement already satisfied: zipp>=0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from importlib-metadata; python_version < "3.8"->markdown->-r py-requirements.txt (line 2)) (3.1.0) + make html pelican /home/cmiss/Jenkins/workspace/PhysiomeJournalSite/content -o /home/cmiss/Jenkins/workspace/PhysiomeJournalSite/output -s /home/cmiss/Jenkins/workspace/PhysiomeJournalSite/pelicanconf.py Done: Processed 5 articles, 0 drafts, 7 pages, 0 hidden pages and 0 draft pages in 1.02 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/journal.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/journal.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/journal.physiomeproject.org/ Sending file modes: C0664 12516 about.html Sink: C0664 12516 about.html Entering directory: D0775 0 archive-descriptions Sending file modes: C0664 3076 test2.json Sink: D0775 0 archive-descriptions Sink: C0664 3076 test2.json Sink: E Sending file modes: C0664 3534 archives.html Sink: C0664 3534 archives.html Entering directory: D0775 0 articles Sending file modes: C0664 6756 incorporation-of-sarcolemmal-calcium-transporters-into-the-shorten-et-al-2007-model-of-skeletal-muscle-equations-coding-and-stability.html Sink: D0775 0 articles Sink: C0664 6756 incorporation-of-sarcolemmal-calcium-transporters-into-the-shorten-et-al-2007-model-of-skeletal-muscle-equations-coding-and-stability.html Sending file modes: C0664 3285 ph-regulation.html Sink: C0664 3285 ph-regulation.html Entering directory: D0775 0 10.6084 Sink: D0775 0 10.6084 Sending file modes: C0664 6666 m9.figshare.c.3841336.html Sink: C0664 6666 m9.figshare.c.3841336.html Sink: E Sending file modes: C0664 4285 cerebral-circulation-model.html Sink: C0664 4285 cerebral-circulation-model.html Sending file modes: C0664 3346 cerebal-circulation-model.html Sink: C0664 3346 cerebal-circulation-model.html Sending file modes: C0664 4119 noble-62-model.html Sink: C0664 4119 noble-62-model.html Sending file modes: C0664 6976 the-cardiac-nak-atpase-an-updated-thermodynamically-consistent-model.html Sink: C0664 6976 the-cardiac-nak-atpase-an-updated-thermodynamically-consistent-model.html Sending file modes: C0664 5417 model-of-skeletal-muscle-cramp-and-its-reversal.html Sink: 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force-dependent-affinity-of-troponin-for-ca2-explains-the-difference-between-the-isotonic-and-isometric-cardiac-end-systolic-force-length-relations.html Entering directory: D0775 0 10.36903 Sending file modes: C0664 8702 physiome.12871364.html Sink: D0775 0 10.36903 Sink: C0664 8702 physiome.12871364.html Sending file modes: C0664 8549 physiome.12871070.html Sink: C0664 8549 physiome.12871070.html Sending file modes: C0664 8374 physiome.12885590.html Sink: C0664 8374 physiome.12885590.html Sending file modes: C0664 8332 physiome.12871022.html Sink: C0664 8332 physiome.12871022.html Sending file modes: C0664 8148 physiome.12859424.html Sink: C0664 8148 physiome.12859424.html Sink: E Sending file modes: C0664 4110 articles.html Sink: E Sink: C0664 4110 articles.html Entering directory: D0775 0 author Sink: D0775 0 author Sending file modes: C0664 12365 the-physiome-project.html Sink: C0664 12365 the-physiome-project.html Sink: E Sending file modes: C0664 3534 authors.html Sink: C0664 3534 authors.html Sending file modes: C0664 3534 categories.html Sink: C0664 3534 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 7840 editorial-board.html Sink: C0664 7840 editorial-board.html Sending file modes: C0664 12365 index.html Sink: C0664 12365 index.html Sending file modes: C0664 23031 instructions-to-authors.html Sink: C0664 23031 instructions-to-authors.html Entering directory: D0775 0 models Entering directory: D0775 0 ccm Sink: D0775 0 models 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 4551 physiome-project.html Sink: C0664 4551 physiome-project.html Sending file modes: C0664 3917 pmr.html Sink: C0664 3917 pmr.html Sending file modes: C0664 3534 tags.html Sink: C0664 3534 tags.html Sending file modes: C0664 4379 testing.html Sink: C0664 4379 testing.html Entering directory: D0775 0 theme Sink: D0775 0 theme Entering directory: D0775 0 js 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 Sink: D0775 0 models Sending file modes: C0664 524257 three.min.js Sink: C0664 524257 three.min.js Sending file modes: C0664 48448 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