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Re: buildbot failure in Yade on yade-full

To: "yade-dev@xxxxxxxxxxxxxxxxxxx" <yade-dev@xxxxxxxxxxxxxxxxxxx>
From: Jerome Duriez <Jerome.Duriez@xxxxxxxxxxx>
Date: Thu, 30 Oct 2014 18:52:26 +0000
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In-reply-to: <909d1329544743e78dac8b71257a24be@BL2FFO11FD041.protection.gbl>
Thread-index: AQHP9GquDT/Cr2foU0Cy/UJ9k13ZGZxI+7hb
Thread-topic: [Yade-dev] buildbot failure in Yade on yade-full

Sorry for that. But it says, it is because of the doc compilation. Here, local run of yadeSphinx.py works without any big problem. See attached file.

I'm working on Ubuntu 14.04, and it's currently quite foggy (tell me what else would be necessary to explain the difference with buildbot..)


________________________________________
From: Yade-dev [yade-dev-bounces+jerome.duriez=ucalgary.ca@xxxxxxxxxxxxxxxxxxx] on behalf of buildbot@xxxxxxxxxxxx [buildbot@xxxxxxxxxxxx]
Sent: October 30, 2014 12:02 PM
To: yade-dev@xxxxxxxxxxxxxxxxxxx
Subject: [Yade-dev] buildbot failure in Yade on yade-full

The Buildbot has detected a failed build on builder yade-full while building yade.
Full details are available at:
 https://yade-dem.org/buildbot/builders/yade-full/builds/2839

Buildbot URL: https://yade-dem.org/buildbot/

Buildslave for this Build: r0calcul5

Build Reason: scheduler
Build Source Stamp: [branch master] 40df7e8944bfafa2d6aac19b837e4a091ea29b34
Blamelist: jduriez <jerome.duriez@xxxxxxxxxxx>

BUILD FAILED: failed shell_2

sincerely,
 -The Buildbot



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duriez@Computer255:~/Yade/trunk/doc/sphinx$ PYTHONPATH=. ~/Yade/install/bin/yadetrunk yadeSphinx.py 
Welcome to Yade 2014-10-30.git-40df7e8 
TCP python prompt on localhost:9000, auth cookie `aedysk'
XMLRPC info provider on http://localhost:21000
Running script yadeSphinx.py
python: warning: unable to convert `\araa'
python: warning: unable to convert `\aj'
python: warning: reference `dec' undefined
python: warning: unable to convert `\aap'
python: warning: reference `aug' undefined
Running Sphinx v1.2.2
WARNING: extension 'youtube' has no setup() function; is it really a Sphinx extension module?
building [html]: all source files
updating environment: 31 added, 0 changed, 0 removed
ERROR /home/duriez/Yade/trunk/pkg/common/InsertionSortCollider.cpp:244 action: verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive verletDist in your script.
/home/duriez/Yade/install/lib/x86_64-linux-gnu/yadetrunk/py/yade/utils.py:63: UserWarning: Overwriting yade.params.ab which already exists.
  if mark in yade.params.__dict__: warnings.warn('Overwriting yade.params.%s which already exists.'%mark)
reading sources... [100%] yade.ymport                                          
/home/duriez/Yade/trunk/doc/sphinx/installation.rst:3: WARNING: Duplicate explicit target name: "github".
/home/duriez/Yade/trunk/doc/sphinx/references.rst:100: WARNING: undecodable source characters, replacing with "?": '.. [Mueller2003] \\ M>>>\xfc<<<ller, Matthias, Charypar, David, Gross, Markus (2003), **Particle-based fluid simulation for interactive applications**. In *Proceedings of the 2003 ACM SIGGRAPH/Eurographics Symposium on Computer Animation*. `(fulltext) <http://dl.acm.org/citation.cfm?id=846276.846298>`__'
/home/duriez/Yade/trunk/doc/sphinx/references.rst:66: WARNING: duplicate citation Jerier2009, other instance in /home/duriez/Yade/trunk/doc/sphinx/publications.rst
/home/duriez/Yade/trunk/doc/sphinx/references.rst:134: WARNING: duplicate citation Scholtes2009b, other instance in /home/duriez/Yade/trunk/doc/sphinx/publications.rst
/home/duriez/Yade/trunk/doc/sphinx/yade.polyhedra_utils.rst:6: WARNING: autodoc: failed to import module u'yade.polyhedra_utils'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 335, in import_object
    __import__(self.modname)
  File "/home/duriez/Yade/install/lib/x86_64-linux-gnu/yadetrunk/py/yade/polyhedra_utils.py", line 20, in <module>
    from yade._polyhedra_utils import *
ImportError: dynamic module does not define init function (init_polyhedra_utils)
/home/duriez/Yade/trunk/doc/sphinx/yade.polyhedra_utils.rst:13: WARNING: autodoc: failed to import module u'yade._polyhedra_utils'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 335, in import_object
    __import__(self.modname)
ImportError: dynamic module does not define init function (init_polyhedra_utils)
/home/duriez/Yade/install/lib/x86_64-linux-gnu/yadetrunk/py/yade/utils.py:docstring of yade.utils.saveVars:10: WARNING: Inline literal start-string without end-string.
/home/duriez/Yade/trunk/doc/sphinx/yade.wrapper.rst:1: WARNING: malformed hyperlink target.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] yade.ymport                                           
/home/duriez/Yade/trunk/doc/sphinx/formulation.rst:733: WARNING: undefined label: sect-calibration-elastic-properties (if the link has no caption the label must precede a section header)
/home/duriez/Yade/trunk/doc/sphinx/formulation.rst:739: WARNING: undefined label: sect-calibration-elastic-properties (if the link has no caption the label must precede a section header)
writing additional files... (17 module code pages) _modules/index genindex py-modindex search index
copying images... [100%] fig/simple-scene-plot-3.png                           
copying static files... 
Exception occurred:
  File "/usr/lib/python2.7/shutil.py", line 69, in copyfile
    raise Error("`%s` and `%s` are the same file" % (src, dst))
Error: `/usr/share/sphinx/themes/basic/static/jquery.js` and `/home/duriez/Yade/trunk/doc/sphinx/_build/html/_static/jquery.js` are the same file
The full traceback has been saved in /tmp/sphinx-err-8hESD3.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks!
Running Sphinx v1.2.2
WARNING: extension 'youtube' has no setup() function; is it really a Sphinx extension module?
building [latex]: all source files
updating environment: 31 added, 0 changed, 0 removed
ERROR /home/duriez/Yade/trunk/pkg/common/InsertionSortCollider.cpp:244 action: verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive verletDist in your script.
reading sources... [100%] yade.ymport                                          
/home/duriez/Yade/trunk/doc/sphinx/installation.rst:3: WARNING: Duplicate explicit target name: "github".
/home/duriez/Yade/trunk/doc/sphinx/references.rst:100: WARNING: undecodable source characters, replacing with "?": '.. [Mueller2003] \\ M>>>\xfc<<<ller, Matthias, Charypar, David, Gross, Markus (2003), **Particle-based fluid simulation for interactive applications**. In *Proceedings of the 2003 ACM SIGGRAPH/Eurographics Symposium on Computer Animation*. `(fulltext) <http://dl.acm.org/citation.cfm?id=846276.846298>`__'
/home/duriez/Yade/trunk/doc/sphinx/references.rst:66: WARNING: duplicate citation Jerier2009, other instance in /home/duriez/Yade/trunk/doc/sphinx/publications.rst
/home/duriez/Yade/trunk/doc/sphinx/references.rst:134: WARNING: duplicate citation Scholtes2009b, other instance in /home/duriez/Yade/trunk/doc/sphinx/publications.rst
/home/duriez/Yade/trunk/doc/sphinx/yade.polyhedra_utils.rst:6: WARNING: autodoc: failed to import module u'yade.polyhedra_utils'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 335, in import_object
    __import__(self.modname)
  File "/home/duriez/Yade/install/lib/x86_64-linux-gnu/yadetrunk/py/yade/polyhedra_utils.py", line 20, in <module>
    from yade._polyhedra_utils import *
ImportError: dynamic module does not define init function (init_polyhedra_utils)
/home/duriez/Yade/trunk/doc/sphinx/yade.polyhedra_utils.rst:13: WARNING: autodoc: failed to import module u'yade._polyhedra_utils'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 335, in import_object
    __import__(self.modname)
ImportError: dynamic module does not define init function (init_polyhedra_utils)
/home/duriez/Yade/install/lib/x86_64-linux-gnu/yadetrunk/py/yade/utils.py:docstring of yade.utils.saveVars:10: WARNING: Inline literal start-string without end-string.
/home/duriez/Yade/trunk/doc/sphinx/yade.wrapper.rst:1: WARNING: malformed hyperlink target.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
WARNING: "latex_documents" config value references unknown document index-toctree_manuals
processing Yade.tex... index-toctree introduction tutorial tutorial-introduction tutorial-hands-on tutorial-data-mining tutorial-geo tutorial-advanced tutorial-examples user prog installation github formulation yade.wrapper modules yade.bodiesHandling yade.export yade.geom yade.linterpolation yade.pack yade.plot yade.polyhedra_utils yade.post2d yade.qt yade.timing yade.utils yade.ymport citing publications references 
resolving references...
None:None: WARNING: undefined label: sect-calibration-elastic-properties (if the link has no caption the label must precede a section header)
None:None: WARNING: undefined label: sect-calibration-elastic-properties (if the link has no caption the label must precede a section header)
writing... /home/duriez/Yade/trunk/doc/sphinx/publications.rst:: WARNING: unusable reference target found: citing.html
/home/duriez/Yade/trunk/doc/sphinx/publications.rst:: WARNING: unusable reference target found: citing.html
done
copying images... fig/qt-gui.png fig/yade-multi-summary.pdf fig/simple-scene-plot-4.pdf fig/simple-scene-plot-1.pdf fig/sweep-and-prune.pdf fig/yade-multi-gnuplot-merged.pdf fig/localstrain.png fig/predicate-difference.png fig/paraview-rendering-apply.png fig/spheres-contact-stiffness.pdf fig/yade-multi-gnuplot-single.pdf fig/funnel.pdf fig/paraview-glyph-icon.png fig/horse.png fig/cell-shear-aabb.pdf fig/yade-iter-loop.pdf fig/dispatch-loop.pdf fig/paraview-open-files.png fig/sphere-sphere.pdf fig/simple-scene-plot-3.pdf fig/hyperboloid.png fig/shear-2d.pdf fig/micro-domains.png fig/cell-flip.pdf fig/spheres-dofs.pdf fig/simple-scene-plot-2.pdf
copying TeX support files...
done
build succeeded, 14 warnings.
Running Sphinx v1.2.2
WARNING: extension 'youtube' has no setup() function; is it really a Sphinx extension module?
building [epub]: all source files
updating environment: 31 added, 0 changed, 0 removed
ERROR /home/duriez/Yade/trunk/pkg/common/InsertionSortCollider.cpp:244 action: verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive verletDist in your script.
reading sources... [100%] yade.ymport                                          
/home/duriez/Yade/trunk/doc/sphinx/installation.rst:3: WARNING: Duplicate explicit target name: "github".
/home/duriez/Yade/trunk/doc/sphinx/references.rst:100: WARNING: undecodable source characters, replacing with "?": '.. [Mueller2003] \\ M>>>\xfc<<<ller, Matthias, Charypar, David, Gross, Markus (2003), **Particle-based fluid simulation for interactive applications**. In *Proceedings of the 2003 ACM SIGGRAPH/Eurographics Symposium on Computer Animation*. `(fulltext) <http://dl.acm.org/citation.cfm?id=846276.846298>`__'
/home/duriez/Yade/trunk/doc/sphinx/references.rst:66: WARNING: duplicate citation Jerier2009, other instance in /home/duriez/Yade/trunk/doc/sphinx/publications.rst
/home/duriez/Yade/trunk/doc/sphinx/references.rst:134: WARNING: duplicate citation Scholtes2009b, other instance in /home/duriez/Yade/trunk/doc/sphinx/publications.rst
/home/duriez/Yade/trunk/doc/sphinx/yade.polyhedra_utils.rst:6: WARNING: autodoc: failed to import module u'yade.polyhedra_utils'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 335, in import_object
    __import__(self.modname)
  File "/home/duriez/Yade/install/lib/x86_64-linux-gnu/yadetrunk/py/yade/polyhedra_utils.py", line 20, in <module>
    from yade._polyhedra_utils import *
ImportError: dynamic module does not define init function (init_polyhedra_utils)
/home/duriez/Yade/trunk/doc/sphinx/yade.polyhedra_utils.rst:13: WARNING: autodoc: failed to import module u'yade._polyhedra_utils'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 335, in import_object
    __import__(self.modname)
ImportError: dynamic module does not define init function (init_polyhedra_utils)
/home/duriez/Yade/install/lib/x86_64-linux-gnu/yadetrunk/py/yade/utils.py:docstring of yade.utils.saveVars:10: WARNING: Inline literal start-string without end-string.
/home/duriez/Yade/trunk/doc/sphinx/yade.wrapper.rst:1: WARNING: malformed hyperlink target.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] yade.ymport                                           
/home/duriez/Yade/trunk/doc/sphinx/formulation.rst:733: WARNING: undefined label: sect-calibration-elastic-properties (if the link has no caption the label must precede a section header)
/home/duriez/Yade/trunk/doc/sphinx/formulation.rst:739: WARNING: undefined label: sect-calibration-elastic-properties (if the link has no caption the label must precede a section header)
writing additional files... (17 module code pages) _modules/index genindex py-modindex search index
copying images... [100%] fig/simple-scene-plot-3.png                           
copying static files... done
copying extra files... done
writing mimetype file...
writing META-INF/container.xml file...
writing content.opf file...
WARNING: unknown mimetype for _images/graphviz-5d54a846fe0904bbc5927f38276fdae17109915e.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-3aca80944cde2986ea886b976d787c38aa17457a.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-cffb6a44905d0e65bce4c8a832c23c374e7e8c58.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-c1b8e11b4ef40761efe771bb966bf1ec27ed93a2.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-f7ff30a21832bbbd06af6b8aea15d2474601e8ed.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-7609762030fafbe20972bbd246f97014f4bd5c56.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-4de0edde5d8d00d4ce156aa3cf1e9323b029b1d5.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-6be6f829cf6ad3cc83af7fc3ac6f2a4e23f27c8b.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-669e3b48b72f02d1f3e758ea5888de0955e246ab.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-5117b966faa3164feb94bb35ac431465e3c95188.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-afefcac7899b283d065e3eb4de79260e6137bdcd.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-26bb3004012b4363ba5e47396a6fb6550e41955c.png.map, ignoring
WARNING: unknown mimetype for _images/cell-shear-aabb.pdf, ignoring
WARNING: unknown mimetype for _images/graphviz-13812a5c39d089fbcab474d893647715d4bda344.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-d60e5008fc3afebda39ea80c4d40f902df18d643.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-f6fce522d4a5af42b53e764b973f456cfa5b1c33.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-82d4aa48fec91098c772dd9750d06cbd39770317.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-af2048d658c2ac9a60c9fd88f3cd506bebe7efc1.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-30b91cbc1494e277b03a6fb9e460bb02dba01d13.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-ba4c41df314b8aaa55b6b02d168f285457e76a30.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-7d5815e19b74c9bafa4e4f324d504ab09b7c0553.png.map, ignoring
WARNING: unknown mimetype for _images/graphviz-5fa8188396c76b59be147d4b8fd4cb1b96c41942.png.map, ignoring
WARNING: unknown mimetype for _static/README, ignoring
WARNING: unknown mimetype for _static/yade-favicon.ico, ignoring
writing toc.ncx file...
writing Yade.epub file...
build succeeded, 35 warnings.
Traceback (most recent call last):
  File "/home/duriez/Yade/install/lib/x86_64-linux-gnu/yadetrunk/py/yade/remote.py", line 123, in run
    Traceback (most recent call last):
  File "/home/duriez/Yade/install/lib/x86_64-linux-gnu/yadetrunk/py/yade/remote.py", line 123, in run
def run(self): self.func()
      File "/usr/lib/python2.7/SocketServer.py", line 235, in serve_forever
def run(self): self.func()
      File "/usr/lib/python2.7/SocketServer.py", line 235, in serve_forever
r, w, e = _eintr_retry(select.select, [self], [], [],
    AttributeError: r, w, e = _eintr_retry(select.select, [self], [], [],
'NoneType' object has no attribute 'select'AttributeError
: 'NoneType' object has no attribute 'select'
duriez@Computer255:~/Yade/trunk/doc/sphinx$

Follow ups

Re: buildbot failure in Yade on yade-full
From: Bruno Chareyre, 2014-10-31