Started by GitHub push by KarinLundengard
Running as SYSTEM
Building remotely on Ubuntu_16.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite
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 fetch --tags --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
> git config remote.origin.url https://github.com/Physiome/journal-website # timeout=10
Fetching upstream changes from https://github.com/Physiome/journal-website
> git fetch --tags --progress -- https://github.com/Physiome/journal-website +refs/heads/*:refs/remotes/origin/* # timeout=10
> git rev-parse refs/remotes/origin/journaldev^{commit} # timeout=10
> git rev-parse refs/remotes/origin/origin/journaldev^{commit} # timeout=10
Checking out Revision c74d9d7e171be0ca3e203a96d769ae1bcf1bfa0f (refs/remotes/origin/journaldev)
> git config core.sparsecheckout # timeout=10
> git checkout -f c74d9d7e171be0ca3e203a96d769ae1bcf1bfa0f # timeout=10
Commit message: "Merge pull request #58 from KarinLundengard/TemporaryStagingForIUPS"
> git rev-list --no-walk 5331f6d0316160f90460acd1bdc7381a7b0f80fa # timeout=10
[Set GitHub commit status (universal)] PENDING on repos [GHRepository@6eed0a16[description=Source for journal.physiomeproject.org.,homepage=<null>,name=journal-website,fork=false,archived=false,size=16438,milestones={},language=HTML,commits={},source=<null>,parent=<null>,responseHeaderFields={null=[HTTP/1.1 200 OK], Access-Control-Allow-Origin=[*], Access-Control-Expose-Headers=[ETag, Link, Location, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval, X-GitHub-Media-Type, Deprecation, Sunset], Cache-Control=[private, max-age=60, s-maxage=60], Content-Encoding=[gzip], Content-Security-Policy=[default-src 'none'], Content-Type=[application/json; charset=utf-8], Date=[Thu, 18 Jun 2020 23:05:50 GMT], ETag=[W/"1864dfc727310ce584b0a10f7f96c6cb"], Last-Modified=[Thu, 18 Jun 2020 23:05:32 GMT], OkHttp-Received-Millis=[1592521550075], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1592521549714], Referrer-Policy=[origin-when-cross-origin, strict-origin-when-cross-origin], Server=[GitHub.com], Status=[200 OK], Strict-Transport-Security=[max-age=31536000; includeSubdomains; preload], Transfer-Encoding=[chunked], Vary=[Accept, Authorization, Cookie, X-GitHub-OTP, Accept-Encoding, Accept, X-Requested-With, Accept-Encoding], X-Accepted-OAuth-Scopes=[repo], X-Content-Type-Options=[nosniff], X-Frame-Options=[deny], X-GitHub-Media-Type=[github.v3; format=json], X-GitHub-Request-Id=[9338:01BC:C3D39:E27E4:5EEBF34D], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4999], X-RateLimit-Reset=[1592525149], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/Physiome/journal-website,id=94735176]] (sha:c74d9d7) with context:journaldev-build
Setting commit status on GitHub for https://github.com/Physiome/journal-website/commit/c74d9d7e171be0ca3e203a96d769ae1bcf1bfa0f
[PhysiomeJournalDevelopmentSite] $ /usr/bin/python2.7 /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9
New python executable in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/bin/python2.7
Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/bin/python
Installing setuptools, pip, wheel...done.
[PhysiomeJournalDevelopmentSite] $ /bin/sh -xe /tmp/shiningpanda5634342448630473255.sh
+ make deps
pip install -r py-requirements.txt
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Collecting pelican>3.6
Using cached pelican-4.2.0-py2.py3-none-any.whl (258 kB)
Collecting markdown
Using cached Markdown-3.1.1-py2.py3-none-any.whl (87 kB)
Collecting six>=1.4
Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Processing /home/cmiss/.cache/pip/wheels/68/1c/e0/44629d259095aa5f4af96d3c4638f46998e4c5b9b02c1cad3f/feedgenerator-1.9.1-py2-none-any.whl
Processing /home/cmiss/.cache/pip/wheels/92/a0/00/8690a57883956a301d91cf4ec999cc0b258b01e3f548f86e89/blinker-1.4-cp27-none-any.whl
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 pytz>=0a
Using cached pytz-2020.1-py2.py3-none-any.whl (510 kB)
Collecting docutils
Using cached docutils-0.16-py2.py3-none-any.whl (548 kB)
Collecting jinja2>=2.7
Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting pygments
Using cached Pygments-2.5.2-py2.py3-none-any.whl (896 kB)
Requirement already satisfied: setuptools>=36 in /home/cmiss/Jenkins/shiningpanda/jobs/888df718/virtualenvs/d41d8cd9/lib/python2.7/site-packages (from markdown->-r py-requirements.txt (line 2)) (44.1.1)
Collecting MarkupSafe>=0.23
Using cached MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl (24 kB)
Installing collected packages: six, pytz, feedgenerator, blinker, unidecode, python-dateutil, docutils, MarkupSafe, jinja2, pygments, pelican, markdown
Successfully installed MarkupSafe-1.1.1 blinker-1.4 docutils-0.16 feedgenerator-1.9.1 jinja2-2.11.2 markdown-3.1.1 pelican-4.2.0 pygments-2.5.2 python-dateutil-2.8.1 pytz-2020.1 six-1.15.0 unidecode-1.1.1
+ make html
pelican /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite/content -o /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite/output -s /home/cmiss/Jenkins/workspace/PhysiomeJournalDevelopmentSite/pelicanconf.py
WARNING: Replacement Indicator '{SITEURL' not recognized, skipping replacement
Done: Processed 3 articles, 0 drafts, 7 pages, 0 hidden pages and 0 draft pages in 0.81 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/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_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/journaldev.physiomeproject.org/
Sending file modes: C0664 12410 about.html
Sink: C0664 12410 about.html
Entering directory: D0775 0 archive-descriptions
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Sending file modes: C0664 3076 test2.json
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Sink: E
Sending file modes: C0664 3874 archives.html
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Entering directory: D0775 0 articles
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Entering directory: D0775 0 10.5072
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Sending file modes: C0664 4450 articles.html
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Entering directory: D0775 0 author
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Sending file modes: C0664 10082 the-physiome-project.html
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Sink: E
Sending file modes: C0664 3874 authors.html
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Sending file modes: C0664 3874 categories.html
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Entering directory: D0775 0 data
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Sending file modes: C0664 625571 nickerson-and-noble-1962.csv
Sink: C0664 625571 nickerson-and-noble-1962.csv
Sink: E
Sending file modes: C0664 8180 editorial-board.html
Sink: C0664 8180 editorial-board.html
Sending file modes: C0664 10082 index.html
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Sending file modes: C0664 22362 instructions-to-authors.html
Sink: C0664 22362 instructions-to-authors.html
Entering directory: D0775 0 models
Sink: D0775 0 models
Entering directory: D0775 0 ccm
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Sending file modes: C0664 449150 nerves_2.json
Sink: C0664 449150 nerves_2.json
Sending file modes: C0664 201 jaw_1.json
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Sending file modes: C0664 3156133 jaw_2.json
Sink: C0664 3156133 jaw_2.json
Sink: E
Sink: E
Entering directory: D0775 0 pdfs
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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 4891 physiome-project.html
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Sending file modes: C0664 4257 pmr.html
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Sending file modes: C0664 3874 tags.html
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Entering directory: D0775 0 theme
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Entering directory: D0775 0 models
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Sink: E
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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 24326372, received 43616 bytes, in 2.0 seconds
Bytes per second: sent 12392345.0, received 22218.9
debug1: Exit status 0
[Set GitHub commit status (universal)] SUCCESS on repos [GHRepository@58fd2a03[description=Source for journal.physiomeproject.org.,homepage=<null>,name=journal-website,fork=false,archived=false,size=16438,milestones={},language=HTML,commits={},source=<null>,parent=<null>,responseHeaderFields={null=[HTTP/1.1 200 OK], Access-Control-Allow-Origin=[*], Access-Control-Expose-Headers=[ETag, Link, Location, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval, X-GitHub-Media-Type, Deprecation, Sunset], Cache-Control=[private, max-age=60, s-maxage=60], Content-Encoding=[gzip], Content-Security-Policy=[default-src 'none'], Content-Type=[application/json; charset=utf-8], Date=[Thu, 18 Jun 2020 23:05:50 GMT], ETag=[W/"1864dfc727310ce584b0a10f7f96c6cb"], Last-Modified=[Thu, 18 Jun 2020 23:05:32 GMT], OkHttp-Received-Millis=[1592521550075], OkHttp-Response-Source=[CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1592521549714], Referrer-Policy=[origin-when-cross-origin, strict-origin-when-cross-origin], Server=[GitHub.com], Status=[200 OK], Strict-Transport-Security=[max-age=31536000; includeSubdomains; preload], Transfer-Encoding=[chunked], Vary=[Accept, Authorization, Cookie, X-GitHub-OTP, Accept-Encoding, Accept, X-Requested-With, Accept-Encoding], X-Accepted-OAuth-Scopes=[repo], X-Content-Type-Options=[nosniff], X-Frame-Options=[deny], X-GitHub-Media-Type=[github.v3; format=json], X-GitHub-Request-Id=[9338:01BC:C3D39:E27E4:5EEBF34D], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4999], X-RateLimit-Reset=[1592525149], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/Physiome/journal-website,id=94735176]] (sha:c74d9d7) with context:journaldev-build
Setting commit status on GitHub for https://github.com/Physiome/journal-website/commit/c74d9d7e171be0ca3e203a96d769ae1bcf1bfa0f
Finished: SUCCESS