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matthiaskoenig / tellurium-web

Tellurium Web Tools
GNU Lesser General Public License v3.0
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CI failing ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.20' not found #33

Closed matthiaskoenig closed 7 years ago

matthiaskoenig commented 7 years ago

Antimony can be installed, but not executed in travis environment.

ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/antimony/_antimony.so)

This works locally. Probably some change in the travis build environment.

 Running setup.py develop for tellurium
Successfully installed MarkupSafe-1.0 amqp-2.2.1 antimony-2.9.3 appdirs-1.4.3 beautifulsoup4-4.6.0 billiard-3.5.0.3 bioservices-1.4.17 bleach-2.0.0 celery-4.1.0 certifi-2017.7.27.1 chardet-3.0.4 colorama-0.3.9 cycler-0.10.0 decorator-4.1.2 django-1.11.5 django-celery-beat-1.0.1 django-celery-results-1.0.1 django-debug-toolbar-1.8 easydev-0.9.35 entrypoints-0.2.3 gevent-1.2.2 greenlet-0.4.12 grequests-0.3.0 html5lib-0.999999999 idna-2.6 ipykernel-4.6.1 ipython-6.1.0 ipython-genutils-0.2.0 ipywidgets-7.0.0 jedi-0.10.2 jinja2-2.9.6 jsonschema-2.6.0 jupyter-client-5.1.0 jupyter-core-4.3.0 kombu-4.1.0 libroadrunner-1.4.18 matplotlib-2.0.2 mistune-0.7.4 nbconvert-5.3.1 nbformat-4.4.0 notebook-5.0.0 pandas-0.20.3 pandocfilters-1.4.2 pexpect-4.2.1 phrasedml-1.0.6 pickleshare-0.7.4 plotly-2.0.15 prompt-toolkit-1.0.15 ptyprocess-0.5.2 pygments-2.2.0 pyparsing-2.2.0 python-dateutil-2.6.1 python-libnuml-1.0.1 python-libsbml-5.15.0 python-libsedml-0.4.1 pytz-2017.2 pyzmq-16.0.2 redis-2.10.6 requests-2.18.4 requests-cache-0.4.13 rrplugins-1.1.8 sbml2matlab-0.9.1 simplegeneric-0.8.1 sqlparse-0.2.3 suds-jurko-0.6 tecombine-0.2.1 tellurium terminado-0.6 testpath-0.3.1 tornado-4.5.2 traitlets-4.3.2 urllib3-1.22 vine-1.1.4 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.0.2 wrapt-1.10.11 xmltodict-0.11.0

travis_time:end:08a0681c:start=1504823563775877936,finish=1504824458359925231,duration=894584047295
travis_fold:end:install.1
travis_fold:start:install.2
travis_time:start:107b9668
$ pip install mock
Requirement already satisfied: mock in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages
Requirement already satisfied: pbr>=0.11 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from mock)
Requirement already satisfied: six>=1.9 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from mock)

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travis_fold:end:install.2
travis_fold:start:install.3
travis_time:start:0cd34184
$ pip install requests
Requirement already satisfied: requests in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from requests)
Requirement already satisfied: idna<2.7,>=2.5 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from requests)
Requirement already satisfied: certifi>=2017.4.17 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from requests)
Requirement already satisfied: urllib3<1.23,>=1.21.1 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from requests)

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travis_fold:end:install.3
travis_fold:start:install.4
travis_time:start:102ae49e
$ pip install coverage
Collecting coverage
  Downloading coverage-4.4.1-cp35-cp35m-manylinux1_x86_64.whl (196kB)
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[?25hInstalling collected packages: coverage
Successfully installed coverage-4.4.1

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travis_fold:end:install.4
travis_fold:start:install.5
travis_time:start:000b0ad8
$ pip install coveralls
Collecting coveralls
  Downloading coveralls-1.2.0-py2.py3-none-any.whl
Requirement already satisfied: coverage>=3.6 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from coveralls)
Collecting docopt>=0.6.1 (from coveralls)
  Downloading docopt-0.6.2.tar.gz
Requirement already satisfied: requests>=1.0.0 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from coveralls)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from requests>=1.0.0->coveralls)
Requirement already satisfied: idna<2.7,>=2.5 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from requests>=1.0.0->coveralls)
Requirement already satisfied: urllib3<1.23,>=1.21.1 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from requests>=1.0.0->coveralls)
Requirement already satisfied: certifi>=2017.4.17 in /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages (from requests>=1.0.0->coveralls)
Building wheels for collected packages: docopt
  Running setup.py bdist_wheel for docopt ... [?25l- done
[?25h  Stored in directory: /home/travis/.cache/pip/wheels/b2/16/5f/c33a2bb5f2dce71205f8e65cbfd05647d79d441282be31fd82
Successfully built docopt
Installing collected packages: docopt, coveralls
Successfully installed coveralls-1.2.0 docopt-0.6.2

travis_time:end:000b0ad8:start=1504824460681453419,finish=1504824462781939528,duration=2100486109
travis_fold:end:install.5
travis_time:start:07651925
$ cd teweb && python manage.py test
Creating test database for alias 'default'...
Traceback (most recent call last):
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/antimony/antimony.py", line 18, in swig_import_helper
    return importlib.import_module(mname)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 986, in _gcd_import
  File "<frozen importlib._bootstrap>", line 969, in _find_and_load
  File "<frozen importlib._bootstrap>", line 958, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 666, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 577, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 914, in create_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/antimony/_antimony.so)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "manage.py", line 22, in <module>
    execute_from_command_line(sys.argv)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/__init__.py", line 364, in execute_from_command_line
    utility.execute()
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/__init__.py", line 356, in execute
    self.fetch_command(subcommand).run_from_argv(self.argv)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/commands/test.py", line 29, in run_from_argv
    super(Command, self).run_from_argv(argv)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/base.py", line 283, in run_from_argv
    self.execute(*args, **cmd_options)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/base.py", line 330, in execute
    output = self.handle(*args, **options)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/commands/test.py", line 62, in handle
    failures = test_runner.run_tests(test_labels)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/test/runner.py", line 602, in run_tests
    self.run_checks()
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/test/runner.py", line 562, in run_checks
    call_command('check', verbosity=self.verbosity)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/__init__.py", line 131, in call_command
    return command.execute(*args, **defaults)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/base.py", line 330, in execute
    output = self.handle(*args, **options)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/commands/check.py", line 68, in handle
    fail_level=getattr(checks, options['fail_level']),
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/base.py", line 359, in check
    include_deployment_checks=include_deployment_checks,
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/management/base.py", line 346, in _run_checks
    return checks.run_checks(**kwargs)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/checks/registry.py", line 81, in run_checks
    new_errors = check(app_configs=app_configs)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/checks/urls.py", line 16, in check_url_config
    return check_resolver(resolver)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/core/checks/urls.py", line 26, in check_resolver
    return check_method()
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/urls/resolvers.py", line 254, in check
    for pattern in self.url_patterns:
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/utils/functional.py", line 35, in __get__
    res = instance.__dict__[self.name] = self.func(instance)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/urls/resolvers.py", line 405, in url_patterns
    patterns = getattr(self.urlconf_module, "urlpatterns", self.urlconf_module)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/utils/functional.py", line 35, in __get__
    res = instance.__dict__[self.name] = self.func(instance)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/urls/resolvers.py", line 398, in urlconf_module
    return import_module(self.urlconf_name)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 986, in _gcd_import
  File "<frozen importlib._bootstrap>", line 969, in _find_and_load
  File "<frozen importlib._bootstrap>", line 958, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 673, in exec_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
  File "/home/travis/build/matthiaskoenig/tellurium-web/teweb/teweb/urls.py", line 27, in <module>
    url(r'^combine/', include('combine.urls')),
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/django/conf/urls/__init__.py", line 50, in include
    urlconf_module = import_module(urlconf_module)
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 986, in _gcd_import
  File "<frozen importlib._bootstrap>", line 969, in _find_and_load
  File "<frozen importlib._bootstrap>", line 958, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 673, in exec_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
  File "/home/travis/build/matthiaskoenig/tellurium-web/teweb/combine/urls.py", line 3, in <module>
    from . import views
  File "/home/travis/build/matthiaskoenig/tellurium-web/teweb/combine/views.py", line 15, in <module>
    from .tasks import add, execute_omex
  File "/home/travis/build/matthiaskoenig/tellurium-web/teweb/combine/tasks.py", line 26, in <module>
    import tellurium
  File "/home/travis/virtualenv/python3.5.3/src/tellurium/tellurium/__init__.py", line 8, in <module>
    from .tellurium import (
  File "/home/travis/virtualenv/python3.5.3/src/tellurium/tellurium/tellurium.py", line 29, in <module>
    import antimony
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/antimony/__init__.py", line 9, in <module>
    from .antimony import *
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/antimony/antimony.py", line 21, in <module>
    _antimony = swig_import_helper()
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/antimony/antimony.py", line 20, in swig_import_helper
    return importlib.import_module('_antimony')
  File "/home/travis/virtualenv/python3.5.3/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ImportError: No module named '_antimony'

travis_time:end:07651925:start=1504824462788221918,finish=1504824464461557271,duration=1673335353

The command "cd teweb && python manage.py test" exited with 1.

Done. Your build exited with 1.
matthiaskoenig commented 7 years ago

Probably due to some build environment upgrade https://docs.travis-ci.com/user/build-environment-updates/2017-09-06/

matthiaskoenig commented 7 years ago 
ImportError: /home/travis/virtualenv/python3.5.3/lib/python3.5/site-packages/antimony/./libcellml.so.2: symbol _ZNSt7__cxx1112basic_stringIwSt11char_traitsIwESaIwEE7reserveEm, version GLIBCXX_3.4.21 not defined in file libstdc++.so.6 with link time reference
matthiaskoenig commented 7 years ago

This is an issue of the wheels which do not build correctly in the travis build environment.

matthiaskoenig commented 7 years ago

Fixed via updated tellurium dependency packages.