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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 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 0e66974c0b753045f84aa2e09654a3e975900805 # timeout=10
[PhysiomeJournalSite] $ /bin/sh -xe /tmp/shiningpanda5775717282273763386.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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 1.06 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-4ubuntu0.3
debug1: match: OpenSSH_8.2p1 Ubuntu-4ubuntu0.3 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/
This account is currently not available.
debug1: client_input_channel_req: channel 0 rtype exit-status reply 0
debug1: client_input_channel_req: channel 0 rtype eow@openssh.com reply 0
debug1: channel 0: free: client-session, nchannels 1
Build step 'Virtualenv Builder' marked build as failure
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: FAILURE