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Started by user David Nickerson 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 210ab9dbe931a579baa887b18035a6278b5c6d2d (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 210ab9dbe931a579baa887b18035a6278b5c6d2d # timeout=10 Commit message: "Merge pull request #172 from Physiome/journaldev" > git rev-list --no-walk 210ab9dbe931a579baa887b18035a6278b5c6d2d # timeout=10 [PhysiomeJournalSite] $ /bin/sh -xe /tmp/shiningpanda10023465574372714699.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)) (4.7.1) 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)) (3.3.6) 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)) (0.18.1) 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)) (1.3.2) 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)) (3.0.3) 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)) (2.0.0) Requirement already satisfied: rich>=10.1 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from pelican>3.6->-r py-requirements.txt (line 1)) (11.0.0) 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)) (2.11.2) 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)) (2021.3) 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)) (2.8.2) 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: importlib-metadata>=4.4 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from markdown->-r py-requirements.txt (line 2)) (4.10.1) 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>=4.4->markdown->-r py-requirements.txt (line 2)) (4.0.1) Requirement already satisfied: zipp>=0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from importlib-metadata>=4.4->markdown->-r py-requirements.txt (line 2)) (3.7.0) 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: six>=1.5 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from python-dateutil>=2.8->pelican>3.6->-r py-requirements.txt (line 1)) (1.16.0) Requirement already satisfied: colorama<0.5.0,>=0.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from rich>=10.1->pelican>3.6->-r py-requirements.txt (line 1)) (0.4.4) Requirement already satisfied: commonmark<0.10.0,>=0.9.0 in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/lib/python3.7/site-packages (from rich>=10.1->pelican>3.6->-r py-requirements.txt (line 1)) (0.9.1) WARNING: You are using pip version 21.3.1; however, version 22.0.4 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 12 articles, 0 drafts, 0 hidden articles, 9 pages, 0 hidden pages and 0 draft pages in 1.11 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_8.2p1 Ubuntu-4ubuntu0.4 debug1: match: OpenSSH_8.2p1 Ubuntu-4ubuntu0.4 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: <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=<ssh-ed25519,sk-ssh-ed25519@openssh.com,ssh-rsa,rsa-sha2-256,rsa-sha2-512,ssh-dss,ecdsa-sha2-nistp256,ecdsa-sha2-nistp384,ecdsa-sha2-nistp521,sk-ecdsa-sha2-nistp256@openssh.com> 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/journal.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 22833 index.html Sink: C0664 22833 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 14965 physiome.16664248.html Sink: C0664 14965 physiome.16664248.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 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 17978 the-physiome-project.html Sink: C0664 17978 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 14806 editorial-board.html Sink: C0664 14806 editorial-board.html Sending file modes: C0664 16116 faqs.html Sink: C0664 16116 faqs.html Sending file modes: C0664 17978 index.html Sink: C0664 17978 index.html Sending file modes: C0664 28426 instructions-to-authors.html Sink: C0664 28426 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 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 10490 testing.html Sink: C0664 10490 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 Sending file modes: C0664 1928 cellml.js Sink: D0775 0 views Sink: C0664 1928 cellml.js Sending file modes: C0664 3673 sedml.js Sink: C0664 3673 sedml.js Sink: E Entering directory: D0775 0 css Sink: E Sending file modes: C0664 0 app.css Sink: D0775 0 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 foundation-icons.ttf Sending file modes: C0664 324210 preview.html Sink: C0664 324210 preview.html Sending file modes: C0664 19508 foundation-icons.css Sink: C0664 19508 foundation-icons.css Sending file modes: C0664 32020 foundation-icons.woff Sink: C0664 32020 foundation-icons.woff Sending file modes: C0664 54568 foundation-icons.eot Sink: C0664 54568 foundation-icons.eot Sending file 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debug1: fd 0 clearing O_NONBLOCK debug1: fd 1 clearing O_NONBLOCK debug1: fd 2 clearing O_NONBLOCK Transferred: sent 24692624, received 45304 bytes, in 1.5 seconds Bytes per second: sent 16829231.8, received 30876.9 debug1: Exit status 0 Sending e-mails to: d.nickerson@auckland.ac.nz karin.lundengard@auckland.ac.nz ERROR: Couldn't connect to host, port: localhost, 25; timeout 60000 com.sun.mail.util.MailConnectException: Couldn't connect to host, port: localhost, 25; timeout 60000; nested exception is: java.net.ConnectException: Connection refused (Connection refused) at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2210) at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:722) at javax.mail.Service.connect(Service.java:342) at javax.mail.Service.connect(Service.java:222) at javax.mail.Service.connect(Service.java:171) at javax.mail.Transport.send0(Transport.java:230) at javax.mail.Transport.send(Transport.java:100) at hudson.tasks.MailSender.run(MailSender.java:131) at hudson.tasks.Mailer.perform(Mailer.java:179) at hudson.tasks.Mailer.perform(Mailer.java:142) at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20) at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:812) at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:761) at hudson.model.Build$BuildExecution.post2(Build.java:178) at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:705) at hudson.model.Run.execute(Run.java:1913) at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43) at hudson.model.ResourceController.execute(ResourceController.java:99) at hudson.model.Executor.run(Executor.java:432) Caused by: java.net.ConnectException: Connection refused (Connection refused) at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:607) at com.sun.mail.util.SocketFetcher.createSocket(SocketFetcher.java:333) at com.sun.mail.util.SocketFetcher.getSocket(SocketFetcher.java:214) at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2160) ... 18 more Finished: SUCCESS