Started by GitHub push by s-fong Running as SYSTEM Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/PhysiomeJournalSite The recommended git tool is: NONE No credentials specified > git rev-parse --resolve-git-dir /home/cmiss/Jenkins/workspace/PhysiomeJournalSite/.git # 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 Checking out Revision c77384cce1b03b191e3dc31d8251329ef8c4a809 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f c77384cce1b03b191e3dc31d8251329ef8c4a809 # timeout=10 Commit message: "Merge pull request #158 from Physiome/journaldev" > git rev-list --no-walk 77fd0fb6e1549e6054faa627a8158ac0abd28713 # timeout=10 [PhysiomeJournalSite] $ /bin/sh -xe /tmp/shiningpanda14985013195412991392.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)) (4.6.0) 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)) (3.3.4) Requirement already satisfied: blinker>=1.4 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: unidecode>=1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (1.2.0) Requirement already satisfied: pygments>=2.6 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (2.9.0) Requirement already satisfied: docutils>=0.16 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (0.17.1) Requirement already satisfied: jinja2>=2.7 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (3.0.1) Requirement already satisfied: python-dateutil>=2.8 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: pytz>=2020.1 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (2021.1) Requirement already satisfied: six in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from feedgenerator>=1.9->pelican>3.6->-r py-requirements.txt (line 1)) (1.16.0) Requirement already satisfied: MarkupSafe>=2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from jinja2>=2.7->pelican>3.6->-r py-requirements.txt (line 1)) (2.0.1) Requirement already satisfied: importlib-metadata in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from markdown->-r py-requirements.txt (line 2)) (4.4.0) Requirement already satisfied: typing-extensions>=3.6.4 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from importlib-metadata->markdown->-r py-requirements.txt (line 2)) (3.10.0.0) Requirement already satisfied: zipp>=0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from importlib-metadata->markdown->-r py-requirements.txt (line 2)) (3.4.1) WARNING: You are using pip version 21.1.2; however, version 21.3.1 is available. You should consider upgrading via the '/home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/bin/python3.7 -m pip install --upgrade pip' command. + 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 11 articles, 0 drafts, 9 pages, 0 hidden pages and 0 draft pages in 1.55 seconds. + scp -v -2 -r -o GlobalKnownHostsFile=**** -i **** output/about.html output/archive-descriptions output/archives.html output/article-prototypes.html output/articles output/author output/authors.html output/categories.html output/contact-us.html output/data output/editorial-board.html output/faqs.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-4ubuntu0.5, 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 [130.216.230.134] 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-4ubuntu0.5 debug1: Remote protocol version 2.0, remote software version OpenSSH_7.6p1 Ubuntu-4ubuntu0.5 debug1: match: OpenSSH_7.6p1 Ubuntu-4ubuntu0.5 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 debug1: kex: host key algorithm: ecdsa-sha2-nistp256 debug1: kex: server->client cipher: chacha20-poly1305@openssh.com MAC: compression: none debug1: kex: client->server cipher: chacha20-poly1305@openssh.com MAC: 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= 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 ([130.216.230.134]: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 19650 about.html Sink: C0664 19650 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 9612 archives.html Sink: C0664 9612 archives.html Sending file modes: C0664 10182 article-prototypes.html Sink: C0664 10182 article-prototypes.html Entering directory: D0775 0 articles Sink: D0775 0 articles Sending file modes: C0664 21386 index.html Sink: C0664 21386 index.html Entering directory: D0775 0 10.36903 Sink: D0775 0 10.36903 Sending file modes: C0664 14872 physiome.12871364.html Sink: C0664 14872 physiome.12871364.html Sending file modes: C0664 14493 physiome.16550526.html Sink: C0664 14493 physiome.16550526.html Sending file modes: C0664 14719 physiome.12871070.html Sink: C0664 14719 physiome.12871070.html Sending file modes: C0664 14544 physiome.12885590.html Sink: C0664 14544 physiome.12885590.html Sending file modes: C0664 13511 physiome.12964970.html Sink: C0664 13511 physiome.12964970.html Sending file modes: C0664 13547 physiome.16828756.html Sink: C0664 13547 physiome.16828756.html Sending file modes: C0664 13189 physiome.16664248.html Sink: C0664 13189 physiome.16664248.html Sending file modes: C0664 14502 physiome.12871022.html Sink: C0664 14502 physiome.12871022.html Sending file modes: C0664 13630 physiome.16590317.html Sink: C0664 13630 physiome.16590317.html Sending file modes: C0664 14318 physiome.12859424.html Sink: C0664 14318 physiome.12859424.html Sending file modes: C0664 14436 physiome.13034423.html Sink: C0664 14436 physiome.13034423.html Sink: E Sink: E Entering directory: D0775 0 author Sink: D0775 0 author Sending file modes: C0664 17864 the-physiome-project.html Sink: C0664 17864 the-physiome-project.html Sink: E Sending file modes: C0664 9612 authors.html Sink: C0664 9612 authors.html Sending file modes: C0664 9612 categories.html Sink: C0664 9612 categories.html Sending file modes: C0664 9777 contact-us.html Sink: C0664 9777 contact-us.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 14507 editorial-board.html Sink: E Sink: C0664 14507 editorial-board.html Sending file modes: C0664 15817 faqs.html Sink: C0664 15817 faqs.html Sending file modes: C0664 17864 index.html Sink: C0664 17864 index.html Sending file modes: C0664 27937 instructions-to-authors.html Sink: C0664 27937 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 10649 physiome-project.html Sink: E Sink: C0664 10649 physiome-project.html Sending file modes: C0664 9995 pmr.html Sink: C0664 9995 pmr.html Sending file modes: C0664 9612 tags.html Sink: C0664 9612 tags.html Sending file modes: C0664 10182 testing.html Sink: C0664 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