Started by user David Nickerson
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 2bc479d5be67a6f0a750a0eeb5d498cdaeb657cb (refs/remotes/origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f 2bc479d5be67a6f0a750a0eeb5d498cdaeb657cb # timeout=10
Commit message: "Merge pull request #77 from Physiome/journaldev"
> git rev-list --no-walk 2bc479d5be67a6f0a750a0eeb5d498cdaeb657cb # timeout=10
[PhysiomeJournalSite] $ /usr/bin/python3.7 /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9
Using base prefix '/usr'
New python executable in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/bin/python3.7
Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenvs/d41d8cd9/bin/python
Installing setuptools, pip, wheel...done.
/home/cmiss/Jenkins/shiningpanda/jobs/1d46dbd3/virtualenv.py:1041: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
[PhysiomeJournalSite] $ /bin/sh -xe /tmp/shiningpanda7549826814034083863.sh
+ make deps
pip install -r py-requirements.txt
Collecting pelican>3.6
Using cached pelican-4.5.0-py2.py3-none-any.whl (673 kB)
Collecting markdown
Using cached Markdown-3.2.2-py3-none-any.whl (88 kB)
Collecting pygments
Using cached Pygments-2.6.1-py3-none-any.whl (914 kB)
Processing /home/cmiss/.cache/pip/wheels/22/f5/18/df711b66eb25b21325c132757d4314db9ac5e8dabeaf196eab/blinker-1.4-py3-none-any.whl
Collecting feedgenerator>=1.9
Using cached feedgenerator-1.9.1-py3-none-any.whl (22 kB)
Collecting jinja2>=2.11
Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting unidecode
Using cached Unidecode-1.1.1-py2.py3-none-any.whl (238 kB)
Collecting python-dateutil
Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting docutils>=0.15
Using cached docutils-0.16-py2.py3-none-any.whl (548 kB)
Collecting pytz>=0a
Using cached pytz-2020.1-py2.py3-none-any.whl (510 kB)
Collecting importlib-metadata; python_version < "3.8"
Using cached importlib_metadata-1.7.0-py2.py3-none-any.whl (31 kB)
Collecting six
Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting MarkupSafe>=0.23
Using cached MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB)
Collecting zipp>=0.5
Using cached zipp-3.1.0-py3-none-any.whl (4.9 kB)
Installing collected packages: pygments, blinker, six, pytz, feedgenerator, MarkupSafe, jinja2, unidecode, python-dateutil, docutils, pelican, zipp, importlib-metadata, markdown
Successfully installed MarkupSafe-1.1.1 blinker-1.4 docutils-0.16 feedgenerator-1.9.1 importlib-metadata-1.7.0 jinja2-2.11.2 markdown-3.2.2 pelican-4.5.0 pygments-2.6.1 python-dateutil-2.8.1 pytz-2020.1 six-1.15.0 unidecode-1.1.1 zipp-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
WARNING: Replacement Indicator '{SITEURL' not recognized, skipping replacement
Done: Processed 5 articles, 0 drafts, 7 pages, 0 hidden pages and 0 draft pages in 1.25 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/
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Entering directory: D0775 0 models
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Entering directory: D0775 0 ccm
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Sink: E
Sink: E
debug1: client_input_channel_req: channel 0 rtype exit-status reply 0
debug1: channel 0: free: client-session, nchannels 1
debug1: fd 0 clearing O_NONBLOCK
debug1: fd 1 clearing O_NONBLOCK
debug1: fd 2 clearing O_NONBLOCK
Transferred: sent 24419268, received 46004 bytes, in 2.1 seconds
Bytes per second: sent 11414249.9, received 21503.6
debug1: Exit status 0
Sending e-mails to: d.nickerson@auckland.ac.nz karin.lundengard@auckland.ac.nz
ERROR: Could not connect to SMTP host: localhost, port: 25
javax.mail.MessagingException: Could not connect to SMTP host: localhost, port: 25;
nested exception is:
java.net.ConnectException: Connection refused (Connection refused)
at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:1934)
at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:638)
at javax.mail.Service.connect(Service.java:295)
at javax.mail.Service.connect(Service.java:176)
at javax.mail.Service.connect(Service.java:125)
at javax.mail.Transport.send0(Transport.java:194)
at javax.mail.Transport.send(Transport.java:124)
at hudson.tasks.MailSender.run(MailSender.java:130)
at hudson.tasks.Mailer.perform(Mailer.java:176)
at hudson.tasks.Mailer.perform(Mailer.java:139)
at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:741)
at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:690)
at hudson.model.Build$BuildExecution.post2(Build.java:186)
at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:635)
at hudson.model.Run.execute(Run.java:1905)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:97)
at hudson.model.Executor.run(Executor.java:428)
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:286)
at com.sun.mail.util.SocketFetcher.getSocket(SocketFetcher.java:231)
at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:1900)
... 18 more
Finished: SUCCESS