Started by GitHub push by nickerso Running as SYSTEM Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite The recommended git tool is: NONE 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 --version # 'git version 2.25.1' > git fetch --tags --force --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 Avoid second fetch > git rev-parse refs/remotes/origin/journaldev^{commit} # timeout=10 Checking out Revision e9a186aa4ebd5ac2e71628a227667bcf5ba7ca5a (refs/remotes/origin/journaldev) > git config core.sparsecheckout # timeout=10 > git checkout -f e9a186aa4ebd5ac2e71628a227667bcf5ba7ca5a # timeout=10 Commit message: "Remove empty author list in primary paper" > git rev-list --no-walk b9d52b6beffd7cb63b3ddf7c67a0a93866c58fb2 # timeout=10 [Set GitHub commit status (universal)] PENDING on repos [] (sha:e9a186a) with context:journaldev-build [PhysiomeJournalDevelopmentSite] $ /usr/bin/python3.7 /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9 Using base prefix '/usr' New python executable in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/bin/python3.7 Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/bin/python Installing setuptools, pip, wheel...done. /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenv.py:1041: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp [PhysiomeJournalDevelopmentSite] $ /bin/sh -xe /tmp/shiningpanda3898443543925159792.sh + make deps pip install -r py-requirements.txt Collecting pelican>3.6 Using cached pelican-4.8.0-py3-none-any.whl (1.4 MB) Collecting markdown Using cached Markdown-3.4.1-py3-none-any.whl (93 kB) Collecting docutils>=0.16 Using cached docutils-0.19-py3-none-any.whl (570 kB) Collecting pytz>=2020.1 Using cached pytz-2022.7.1-py2.py3-none-any.whl (499 kB) Collecting rich>=10.1 Using cached rich-13.2.0-py3-none-any.whl (238 kB) Collecting blinker>=1.4 Using cached blinker-1.5-py2.py3-none-any.whl (12 kB) Collecting python-dateutil>=2.8 Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting pygments>=2.6 Using cached Pygments-2.14.0-py3-none-any.whl (1.1 MB) Collecting jinja2>=2.7 Using cached Jinja2-3.1.2-py3-none-any.whl (133 kB) Collecting feedgenerator>=1.9 Using cached feedgenerator-2.0.0-py3-none-any.whl (21 kB) Collecting unidecode>=1.1 Using cached Unidecode-1.3.6-py3-none-any.whl (235 kB) Collecting importlib-metadata>=4.4 Using cached importlib_metadata-6.0.0-py3-none-any.whl (21 kB) Collecting typing-extensions>=3.6.4 Using cached typing_extensions-4.4.0-py3-none-any.whl (26 kB) Collecting zipp>=0.5 Using cached zipp-3.11.0-py3-none-any.whl (6.6 kB) Collecting MarkupSafe>=2.0 Using cached MarkupSafe-2.1.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting six>=1.5 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting markdown-it-py<3.0.0,>=2.1.0 Using cached markdown_it_py-2.1.0-py3-none-any.whl (84 kB) Collecting mdurl~=0.1 Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB) Installing collected packages: pytz, zipp, unidecode, typing-extensions, six, pygments, mdurl, MarkupSafe, feedgenerator, docutils, blinker, python-dateutil, markdown-it-py, jinja2, importlib-metadata, rich, markdown, pelican Successfully installed MarkupSafe-2.1.2 blinker-1.5 docutils-0.19 feedgenerator-2.0.0 importlib-metadata-6.0.0 jinja2-3.1.2 markdown-3.4.1 markdown-it-py-2.1.0 mdurl-0.1.2 pelican-4.8.0 pygments-2.14.0 python-dateutil-2.8.2 pytz-2022.7.1 rich-13.2.0 six-1.16.0 typing-extensions-4.4.0 unidecode-1.3.6 zipp-3.11.0 + 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 16 articles, 0 drafts, 0 hidden articles, 9 pages, 0 hidden pages and 0 draft pages in 0.53 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/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_8.2p1 Ubuntu-4ubuntu0.5, OpenSSL 1.1.1f 31 Mar 2020 debug1: Reading configuration data /etc/ssh/ssh_config debug1: /etc/ssh/ssh_config line 19: include /etc/ssh/ssh_config.d/*.conf matched no files debug1: /etc/ssh/ssh_config line 21: Applying options for * debug1: Connecting to abiwebsrv02.bioeng.auckland.ac.nz [130.216.230.134] port 22. debug1: Connection established. debug1: identity file **** type -1 debug1: identity file ****-cert type -1 debug1: Local version string SSH-2.0-OpenSSH_8.2p1 Ubuntu-4ubuntu0.5 debug1: Remote protocol version 2.0, remote software version OpenSSH_8.2p1 Ubuntu-4ubuntu0.5 debug1: match: OpenSSH_8.2p1 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 out after 134217728 blocks debug1: SSH2_MSG_NEWKEYS sent debug1: expecting SSH2_MSG_NEWKEYS debug1: SSH2_MSG_NEWKEYS received debug1: rekey in after 134217728 blocks debug1: Will attempt key: **** explicit 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: Remote: /home/pj-site/.ssh/authorized_keys:1: key options: agent-forwarding port-forwarding pty user-rc x11-forwarding 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 19801 about.html Sink: C0664 19801 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 9621 archives.html Sink: C0664 9621 archives.html Sending file modes: C0664 10191 article-prototypes.html Sink: C0664 10191 article-prototypes.html Entering directory: D0775 0 articles Sink: D0775 0 articles Sending file modes: C0664 27920 index.html Sink: C0664 27920 index.html Entering directory: D0775 0 10.36903 Sink: D0775 0 10.36903 Sending file modes: C0664 17280 physiome.12871364.html Sink: C0664 17280 physiome.12871364.html Sending file modes: C0664 20855 physiome.16550526.html Sink: C0664 20855 physiome.16550526.html Sending file modes: C0664 18993 physiome.12871070.html Sink: C0664 18993 physiome.12871070.html Sending file modes: C0664 18876 physiome.12885590.html Sink: C0664 18876 physiome.12885590.html Sending file modes: C0664 16282 physiome.12964970.html Sink: C0664 16282 physiome.12964970.html Sending file modes: C0664 15489 physiome.16828756.html Sink: C0664 15489 physiome.16828756.html Sending file modes: C0664 14733 physiome.21708179.html Sink: C0664 14733 physiome.21708179.html Sending file modes: C0664 14300 physiome.21708176.html Sink: C0664 14300 physiome.21708176.html Sending file modes: C0664 14965 physiome.16664248.html Sink: C0664 14965 physiome.16664248.html Sending file modes: C0664 14382 physiome.21714863.html Sink: C0664 14382 physiome.21714863.html Sending file modes: C0664 25287 physiome.12871022.html Sink: C0664 25287 physiome.12871022.html Sending file modes: C0664 15254 physiome.16590317.html Sink: C0664 15254 physiome.16590317.html Sending file modes: C0664 18458 physiome.19070171.html Sink: C0664 18458 physiome.19070171.html Sending file modes: C0664 15642 physiome.12859424.html Sink: C0664 15642 physiome.12859424.html Sending file modes: C0664 13730 physiome.21760691.html Sink: C0664 13730 physiome.21760691.html Sending file modes: C0664 17573 physiome.13034423.html Sink: C0664 17573 physiome.13034423.html Sink: E Sink: E Entering directory: D0775 0 author Sink: D0775 0 author Sending file modes: C0664 19518 the-physiome-project.html Sink: C0664 19518 the-physiome-project.html Sink: E Sending file modes: C0664 9621 authors.html Sink: C0664 9621 authors.html Sending file modes: C0664 9621 categories.html Sink: C0664 9621 categories.html Sending file modes: C0664 9919 contact-us.html Sink: C0664 9919 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 Sink: E Sending file modes: C0664 14946 editorial-board.html Sink: C0664 14946 editorial-board.html Sending file modes: C0664 16116 faqs.html Sink: C0664 16116 faqs.html Sending file modes: C0664 19518 index.html Sink: C0664 19518 index.html Sending file modes: C0664 28922 instructions-to-authors.html Sink: C0664 28922 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 10817 physiome-project.html Sink: C0664 10817 physiome-project.html Sending file modes: C0664 10160 pmr.html Sink: C0664 10160 pmr.html Sending file modes: C0664 9621 tags.html Sink: C0664 9621 tags.html Sending file modes: C0664 10444 testing.html Sink: C0664 10444 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 1928 cellml.js Sink: C0664 1928 cellml.js Sending file modes: C0664 3673 sedml.js Sink: C0664 3673 sedml.js Sink: E Sink: E Entering directory: D0775 0 css Sink: D0775 0 css Sending file modes: C0664 0 app.css Sink: C0664 0 app.css Sending file modes: C0664 110693 foundation.css Sink: C0664 110693 foundation.css Entering directory: D0775 0 foundation-icons Sink: D0775 0 foundation-icons Sending file modes: C0664 56976 foundation-icons.ttf Sink: C0664 56976 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