Started by upstream project "OpenCOR_Linux" build number 1150
originally caused by:
 GitHub pull request #2411 of commit a52f09de41e08d52557465c8e1e8471dbe75a9c2, no merge conflicts.
Running as SYSTEM
Building remotely on Ubuntu_16.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/OpenCOR_Linux/Slave/Ubuntu_16.04_bioeng49
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/opencor/opencor.git # timeout=10
Fetching upstream changes from https://github.com/opencor/opencor.git
 > git --version # timeout=10
 > git --version # 'git version 2.17.1'
 > git fetch --tags --progress -- https://github.com/opencor/opencor.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=10
JENKINS-19022: warning: possible memory leak due to Git plugin usage; see: https://wiki.jenkins.io/display/JENKINS/Remove+Git+Plugin+BuildsByBranch+BuildData
Checking out Revision 0c0a0c3aabcc131141a9e6d2a304480df94bf875 (refs/remotes/origin/pr/2411/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 0c0a0c3aabcc131141a9e6d2a304480df94bf875 # timeout=10
Commit message: "Merge a52f09de41e08d52557465c8e1e8471dbe75a9c2 into 5a13167dbd47e74e0941dbd65e6e387cff31c258"
 > git rev-list --no-walk 1cd1c6cb3e2a737aa1ce34ab8cc313f40d092e76 # timeout=10
[Ubuntu_16.04_bioeng49] $ /bin/sh -xe /tmp/jenkins7020452740821276528.sh
+ pip3 list
DEPRECATION: The default format will switch to columns in the future. You can use --format=(legacy|columns) (or define a format=(legacy|columns) in your pip.conf under the [list] section) to disable this warning.
alabaster (0.7.8)
apturl (0.5.2)
asn1crypto (0.24.0)
attrs (17.4.0)
Automat (0.6.0)
Babel (2.4.0)
beautifulsoup4 (4.6.0)
blinker (1.4)
Brlapi (0.6.6)
buildbot-worker (1.1.1-3ubuntu5)
certifi (2018.1.18)
chardet (3.0.4)
checkbox-support (0.22)
click (6.7)
colorama (0.3.7)
command-not-found (0.3)
constantly (15.1.0)
cryptography (2.1.4)
cupshelpers (1.0)
defer (1.0.6)
distro-info (0.18ubuntu0.18.04.1)
docutils (0.14)
feedparser (5.2.1)
future (0.15.2)
guacamole (0.9.2)
html5lib (0.999999999)
httplib2 (0.9.2)
hyperlink (17.3.1)
idna (2.6)
imagesize (0.7.1)
incremental (16.10.1)
Jinja2 (2.10)
keyring (10.6.0)
keyrings.alt (3.0)
language-selector (0.1)
launchpadlib (1.10.6)
lazr.restfulclient (0.13.5)
lazr.uri (1.0.3)
louis (3.5.0)
lxml (4.2.1)
macaroonbakery (1.1.3)
Mako (1.0.7)
MarkupSafe (1.0)
netifaces (0.10.4)
numpy (1.13.3)
oauth (1.0.1)
oauthlib (2.0.6)
olefile (0.45.1)
onboard (1.4.1)
padme (1.1.1)
PAM (0.4.2)
pexpect (4.2.1)
Pillow (5.1.0)
pip (9.0.1)
plainbox (0.25)
protobuf (3.0.0)
pyasn1 (0.4.2)
pyasn1-modules (0.2.1)
pycairo (1.16.2)
pycrypto (2.6.1)
pycups (1.9.73)
pycurl (7.43.0.1)
Pygments (2.2.0)
pygobject (3.26.1)
PyJWT (1.5.3)
pymacaroons (0.13.0)
PyNaCl (1.1.2)
pyOpenSSL (17.5.0)
pyparsing (2.2.0)
pyRFC3339 (1.0)
pyserial (3.4)
python-apt (1.6.5+ubuntu0.3)
python-dateutil (2.6.1)
python-debian (0.1.32)
pytz (2018.3)
pyxdg (0.25)
PyYAML (3.12)
reportlab (3.4.0)
requests (2.18.4)
requests-unixsocket (0.1.5)
roman (2.0.0)
SecretStorage (2.3.1)
service-identity (16.0.0)
setuptools (39.0.1)
simplejson (3.13.2)
six (1.11.0)
Sphinx (1.6.7)
ssh-import-id (5.7)
system-service (0.3)
systemd-python (234)
Twisted (17.9.0)
ubuntu-drivers-common (0.0.0)
ufw (0.36)
unattended-upgrades (0.1)
unity-scope-calculator (0.1)
unity-scope-chromiumbookmarks (0.1)
unity-scope-colourlovers (0.1)
unity-scope-devhelp (0.1)
unity-scope-firefoxbookmarks (0.1)
unity-scope-manpages (0.1)
unity-scope-openclipart (0.1)
unity-scope-texdoc (0.1)
unity-scope-tomboy (0.1)
unity-scope-virtualbox (0.1)
unity-scope-yelp (0.1)
unity-scope-zotero (0.1)
urllib3 (1.22)
usb-creator (0.3.3)
virtualenv (15.1.0)
wadllib (1.3.2)
webencodings (0.5)
wheel (0.30.0)
xdiagnose (3.8.8)
xkit (0.0.0)
XlsxWriter (0.9.6)
zope.interface (4.3.2)
+ pip3 install pygit2
Collecting pygit2
  Downloading https://files.pythonhosted.org/packages/20/02/25077cf7ac6599e0e6bd2c6836e7c7360244d2d7224d54e51218dbe00711/pygit2-1.3.0.tar.gz (243kB)
Collecting cached-property (from pygit2)
  Downloading https://files.pythonhosted.org/packages/48/19/f2090f7dad41e225c7f2326e4cfe6fff49e57dedb5b53636c9551f86b069/cached_property-1.5.2-py2.py3-none-any.whl
Collecting cffi>=1.4.0 (from pygit2)
  Downloading https://files.pythonhosted.org/packages/50/ca/bbca0fd95b24a1d4f0d2e016f09f35ae68d4fe72bf34cc538d0a0d2d3e10/cffi-1.14.3-cp36-cp36m-manylinux1_x86_64.whl (400kB)
Collecting pycparser (from cffi>=1.4.0->pygit2)
  Downloading https://files.pythonhosted.org/packages/ae/e7/d9c3a176ca4b02024debf82342dab36efadfc5776f9c8db077e8f6e71821/pycparser-2.20-py2.py3-none-any.whl (112kB)
Building wheels for collected packages: pygit2
  Running setup.py bdist_wheel for pygit2: started
  Running setup.py bdist_wheel for pygit2: finished with status 'error'
  Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-elkabtp5/pygit2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmpukyiwpiepip-wheel- --python-tag cp36:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.6
  creating build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/credentials.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/ffi.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/refspec.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/submodule.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/errors.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/callbacks.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/_build.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/remote.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/repository.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/utils.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/config.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/__init__.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/_run.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/index.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/settings.py -> build/lib.linux-x86_64-3.6/pygit2
  copying pygit2/blame.py -> build/lib.linux-x86_64-3.6/pygit2
  creating build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/revert.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/describe.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/common.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/merge.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/errors.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/indexer.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/blame.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/submodule.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/types.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/index.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/graph.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/pack.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/callbacks.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/repository.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/checkout.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/remote.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/diff.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/strarray.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/transport.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/proxy.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/stash.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/clone.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/config.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/net.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/oid.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/refspec.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/attr.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  copying pygit2/decl/buffer.h -> build/lib.linux-x86_64-3.6/pygit2/decl
  running build_ext
  generating cffi module 'build/temp.linux-x86_64-3.6/pygit2._libgit2.c'
  creating build/temp.linux-x86_64-3.6
  building 'pygit2._pygit2' extension
  creating build/temp.linux-x86_64-3.6/src
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/usr/include/python3.6m -c src/blob.c -o build/temp.linux-x86_64-3.6/src/blob.o
  In file included from src/blob.h:34:0,
                   from src/blob.c:30:
  src/types.h:36:2: error: #error You need a compatible libgit2 version (1.0.x)
   #error You need a compatible libgit2 version (1.0.x)
    ^~~~~
  src/types.h:258:5: error: unknown type name ‘git_mailmap’
       git_mailmap *mailmap;
       ^~~~~~~~~~~
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  
  ----------------------------------------
  Failed building wheel for pygit2
  Running setup.py clean for pygit2
Failed to build pygit2
Installing collected packages: cached-property, pycparser, cffi, pygit2
  Running setup.py install for pygit2: started
    Running setup.py install for pygit2: finished with status 'error'
    Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-elkabtp5/pygit2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-jgepfuzh-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/credentials.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/ffi.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/refspec.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/submodule.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/errors.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/callbacks.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/_build.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/remote.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/repository.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/utils.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/config.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/__init__.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/_run.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/index.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/settings.py -> build/lib.linux-x86_64-3.6/pygit2
    copying pygit2/blame.py -> build/lib.linux-x86_64-3.6/pygit2
    creating build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/revert.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/describe.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/common.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/merge.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/errors.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/indexer.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/blame.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/submodule.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/types.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/index.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/graph.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/pack.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/callbacks.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/repository.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/checkout.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/remote.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/diff.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/strarray.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/transport.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/proxy.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/stash.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/clone.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/config.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/net.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/oid.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/refspec.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/attr.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    copying pygit2/decl/buffer.h -> build/lib.linux-x86_64-3.6/pygit2/decl
    running build_ext
    generating cffi module 'build/temp.linux-x86_64-3.6/pygit2._libgit2.c'
    creating build/temp.linux-x86_64-3.6
    building 'pygit2._pygit2' extension
    creating build/temp.linux-x86_64-3.6/src
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/usr/include/python3.6m -c src/blob.c -o build/temp.linux-x86_64-3.6/src/blob.o
    In file included from src/blob.h:34:0,
                     from src/blob.c:30:
    src/types.h:36:2: error: #error You need a compatible libgit2 version (1.0.x)
     #error You need a compatible libgit2 version (1.0.x)
      ^~~~~
    src/types.h:258:5: error: unknown type name ‘git_mailmap’
         git_mailmap *mailmap;
         ^~~~~~~~~~~
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    
    ----------------------------------------
Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-elkabtp5/pygit2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-jgepfuzh-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-elkabtp5/pygit2/
Build step 'Execute shell' marked build as failure
[Set GitHub commit status (universal)] ERROR on repos [GHRepository@18ddb207[nodeId=MDEwOlJlcG9zaXRvcnk5OTU3NjY3,description=OpenCOR is a cross-platform modelling environment, which can be used to organise, edit, simulate and analyse CellML files.,homepage=https://opencor.ws/,name=opencor,fork=false,archived=false,size=176097,milestones={},language=C++,commits={},source=<null>,parent=<null>,isTemplate=<null>,url=https://api.github.com/repos/opencor/opencor,id=9957667,nodeId=<null>,createdAt=2013-05-09T11:07:58Z,updatedAt=2020-10-11T23:37:46Z]] (sha:0c0a0c3) with context:OpenCOR_Linux/Slave=Ubuntu_16.04_bioeng49
Setting commit status on GitHub for https://github.com/opencor/opencor/commit/0c0a0c3aabcc131141a9e6d2a304480df94bf875
Finished: FAILURE