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[Question #163713]: Problems with scons PREFIX=/home/daniela/YADE

To: yade-users@xxxxxxxxxxxxxxxxxxx
From: Daniela <question163713@xxxxxxxxxxxxxxxxxxxxx>
Date: Mon, 04 Jul 2011 13:50:55 -0000
Reply-to: question163713@xxxxxxxxxxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx
New question #163713 on Yade:
https://answers.launchpad.net/yade/+question/163713

Hi!
I'm trying to install Yade, but I cannot understand what is going wrong with it. 
At the end of the compilation it shows messages like "scons: *** Found dependency cycle(s):" and many "internal erros".
Could someone please help me solving this problem?
Thanks a lot. Daniela.

scons: Reading SConscript files ...
@@@ Using profile default (scons.profile-default) @@@
Eigen 2 math library will be used
Yade version is `bzr2880' (bzr2880), installed files will be suffixed with `-bzr2880'.
All intermediary files will be in `/home/dmaionchi/build-bzr2880'.
Mkdir("/home/dmaionchi/build-bzr2880")
Checking whether c++ compiler "g++" works...yes
Finding libstdc++ library... (cached) /usr/lib/libstdc++.so.6
Checking for pthread_exit(NULL) in C library pthread... yes
Checking for Python development files... ok
Checking for C++ header file numpy/ndarrayobject.h... yes
Checking for required python modules... (cached) all ok
Checking boost libraries... all ok
Checking for C++ header file boost/foreach.hpp... yes
Checking for C++ header file Eigen/Core... yes
Checking for C++ header file loki/NullType.h... yes
Checking for glutGetModifiers() in C++ library glut... yes
Checking for QGLViewer() in C++ library qglviewer-qt4... yes
Checking for vtkInstantiator::New() in C++ library vtkCommon... yes
Checking for gts_object_class() in C++ library gts... yes
Checking for log4cxx::Logger::getLogger("") in C++ library log4cxx... yes
Deleting extra plugin /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkList.py
Deleting extra plugin /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkWeight.py
Deleting extra plugin /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkTestNormalInelasticity.py
Deleting extra plugin /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkTestDummy.py
Deleting extra plugin /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkTestTriax.py
Deleting extra plugin /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/data/checkTestTriax.spheres
Deleting extra plugin /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/data/WallStressesCheckTest
scons: done reading SConscript files.
scons: Building targets ...
> /home/dmaionchi/YADE/bin/yade-bzr2880
Chmod("/home/dmaionchi/YADE/bin/yade-bzr2880", 0755)
> /home/dmaionchi/YADE/bin/yade-bzr2880-batch
Chmod("/home/dmaionchi/YADE/bin/yade-bzr2880-batch", 0755)
C py/3rd-party/pygts-0.3.1/cleanup.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/cleanup.c:36:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
C py/3rd-party/pygts-0.3.1/face.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/face.c:28:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
C py/3rd-party/pygts-0.3.1/edge.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/edge.c:28:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
C py/3rd-party/pygts-0.3.1/object.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/object.c:28:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
C py/3rd-party/pygts-0.3.1/point.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/point.c:28:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
C py/3rd-party/pygts-0.3.1/pygts.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/pygts.c:28:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
C py/3rd-party/pygts-0.3.1/segment.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/segment.c:28:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
C py/3rd-party/pygts-0.3.1/surface.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/surface.c:28:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
C py/3rd-party/pygts-0.3.1/triangle.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/triangle.c:28:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
C py/3rd-party/pygts-0.3.1/vertex.c
In file included from /usr/include/python2.6/Python.h:8,
                 from py/3rd-party/pygts-0.3.1/pygts.h:39,
                 from py/3rd-party/pygts-0.3.1/vertex.c:28:
/usr/include/python2.6/pyconfig.h:1031: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:213: note: this is the location of the previous definition
> /home/dmaionchi/build-bzr2880/lib/yade-support.cpp
C /home/dmaionchi/build-bzr2880/lib/yade-support.cpp
In file included from /usr/include/boost/python/object/function_handle.hpp:10,
                 from /usr/include/boost/python/converter/arg_to_python.hpp:19,
                 from /usr/include/boost/python/call.hpp:15,
                 from /usr/include/boost/python/object_core.hpp:12,
                 from /usr/include/boost/python/args.hpp:25,
                 from /usr/include/boost/python.hpp:11,
                 from /home/dmaionchi/yade/lib/serialization/Serializable.hpp:23,
                 from /home/dmaionchi/yade/lib/serialization/Serializable.cpp:11,
                 from /home/dmaionchi/build-bzr2880/lib/yade-support.cpp:5:
/home/dmaionchi/yade/lib/serialization/Serializable.hpp: In member function 'PyObject* boost::python::objects::caller_py_function_impl<Caller>::operator()(PyObject*, PyObject*) [with Caller = boost::python::detail::caller<PyObject* (*)(Serializable&, const Serializable&), boost::python::default_call_policies, boost::mpl::vector3<PyObject*, Serializable&, const Serializable&> >]':
/home/dmaionchi/yade/lib/serialization/Serializable.hpp:262: warning: dereferencing pointer 'p.2704' does break strict-aliasing rules
/usr/include/boost/python/detail/destroy.hpp:90: note: initialized from here
/home/dmaionchi/build-bzr2880/include/yade/lib/factory/Factorable.hpp:63: warning: dereferencing pointer 'this.691' does break strict-aliasing rules
/home/dmaionchi/yade/lib/serialization/Serializable.hpp:262: note: initialized from here
/home/dmaionchi/yade/lib/serialization/Serializable.hpp:262: warning: dereferencing pointer 'p.2704' does break strict-aliasing rules
/usr/include/boost/python/detail/destroy.hpp:90: note: initialized from here
/home/dmaionchi/build-bzr2880/include/yade/lib/factory/Factorable.hpp:63: warning: dereferencing pointer 'this.691' does break strict-aliasing rules
/home/dmaionchi/yade/lib/serialization/Serializable.hpp:262: note: initialized from here
L libyade-support.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/lib/libyade-support.so
L _gts.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/gts/_gts.so
ln -s -f ../py/gts/_gts.so /home/dmaionchi/YADE/lib/yade-bzr2880/lib/lib_gts__python-module.so
> /home/dmaionchi/build-bzr2880/core/core.cpp
C /home/dmaionchi/build-bzr2880/core/core.cpp
L libcore.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/lib/libcore.so
C pkg/common/Aabb.cpp
L libAabb.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libAabb.so
C pkg/common/Bo1_Box_Aabb.cpp
C pkg/common/Box.cpp
L libBox.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libBox.so
C pkg/common/Dispatching.cpp
C pkg/common/VelocityBins.cpp
L libVelocityBins.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libVelocityBins.so
L libDispatching.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libDispatching.so
L libBo1_Box_Aabb.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libBo1_Box_Aabb.so
C pkg/common/Bo1_Facet_Aabb.cpp
C pkg/common/Facet.cpp
L libFacet.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libFacet.so
L libBo1_Facet_Aabb.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libBo1_Facet_Aabb.so
C pkg/common/Bo1_Sphere_Aabb.cpp
C pkg/common/Sphere.cpp
L libSphere.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libSphere.so
L libBo1_Sphere_Aabb.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libBo1_Sphere_Aabb.so
C pkg/common/BoundaryController.cpp
L libBoundaryController.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libBoundaryController.so
C pkg/common/Callbacks.cpp
L libCallbacks.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCallbacks.so
C pkg/dem/CapillaryPhys.cpp
C pkg/dem/FrictPhys.cpp
C pkg/common/NormShearPhys.cpp
L libNormShearPhys.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libNormShearPhys.so
L libFrictPhys.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libFrictPhys.so
L libCapillaryPhys.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCapillaryPhys.so
C pkg/dem/CapillaryStressRecorder.cpp
C pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity.cpp
C pkg/common/ElastMat.cpp
L libElastMat.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libElastMat.so
C pkg/dem/ScGeom.cpp
C pkg/dem/DemXDofGeom.cpp
L libDemXDofGeom.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libDemXDofGeom.so
L libScGeom.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libScGeom.so
L libLaw2_ScGeom_CapillaryPhys_Capillarity.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libLaw2_ScGeom_CapillaryPhys_Capillarity.so
C pkg/dem/TriaxialCompressionEngine.cpp
C pkg/dem/Shop.cpp
C pkg/dem/Tetra.cpp
L libTetra.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libTetra.so
C pkg/dem/ViscoelasticPM.cpp
L libViscoelasticPM.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libViscoelasticPM.so
C pkg/common/Gl1_NormPhys.cpp
C pkg/common/GLDrawFunctors.cpp
L libGLDrawFunctors.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGLDrawFunctors.so
C pkg/common/OpenGLRenderer.cpp
L libOpenGLRenderer.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libOpenGLRenderer.so
C pkg/common/MatchMaker.cpp
L libMatchMaker.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libMatchMaker.so
C pkg/common/InsertionSortCollider.cpp
C pkg/common/Collider.cpp
L libCollider.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCollider.so
C pkg/dem/NewtonIntegrator.cpp
^FompC pkg/dem/Clump.cpp
L libClump.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libClump.so
L libNewtonIntegrator.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libNewtonIntegrator.so
L libInsertionSortCollider.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libInsertionSortCollider.so
C pkg/dem/Ig2_Sphere_Sphere_ScGeom.cpp
L libIg2_Sphere_Sphere_ScGeom.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libIg2_Sphere_Sphere_ScGeom.so
C pkg/common/GravityEngines.cpp
C pkg/common/FieldApplier.cpp
L libFieldApplier.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libFieldApplier.so
C pkg/common/PeriodicEngines.cpp
L libPeriodicEngines.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libPeriodicEngines.so
L libGravityEngines.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGravityEngines.so
C pkg/dem/Ip2_FrictMat_FrictMat_FrictPhys.cpp
L libIp2_FrictMat_FrictMat_FrictPhys.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libIp2_FrictMat_FrictMat_FrictPhys.so
C pkg/dem/GlobalStiffnessTimeStepper.cpp
L libGlobalStiffnessTimeStepper.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGlobalStiffnessTimeStepper.so
C pkg/common/InteractionLoop.cpp
L libInteractionLoop.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libInteractionLoop.so
C pkg/dem/ElasticContactLaw.cpp
L libElasticContactLaw.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libElasticContactLaw.so
C pkg/dem/Ig2_Box_Sphere_ScGeom.cpp
L libIg2_Box_Sphere_ScGeom.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libIg2_Box_Sphere_ScGeom.so
C pkg/common/ForceResetter.cpp
L libForceResetter.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libForceResetter.so
C pkg/dem/TriaxialStressController.cpp
C pkg/common/Recorder.cpp
L libRecorder.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libRecorder.so
C pkg/dem/CapillaryTriaxialTest.cpp
C pkg/dem/Ip2_FrictMat_FrictMat_CapillaryPhys.cpp
L libIp2_FrictMat_FrictMat_CapillaryPhys.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libIp2_FrictMat_FrictMat_CapillaryPhys.so
C pkg/dem/TriaxialStateRecorder.cpp
C pkg/dem/CohFrictMat.cpp
L libCohFrictMat.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCohFrictMat.so
C pkg/dem/CohFrictPhys.cpp
L libCohFrictPhys.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCohFrictPhys.so
C pkg/dem/CohesionlessMomentRotation.cpp
L libCohesionlessMomentRotation.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCohesionlessMomentRotation.so
C pkg/dem/CohesiveFrictionalContactLaw.cpp
L libCohesiveFrictionalContactLaw.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCohesiveFrictionalContactLaw.so
C pkg/dem/CohesiveFrictionalPM.cpp
L libCohesiveFrictionalPM.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCohesiveFrictionalPM.so
C pkg/dem/CohesiveStateRPMRecorder.cpp
C pkg/dem/RockPM.cpp
C pkg/dem/CohesiveTriaxialTest.cpp
C pkg/dem/Ip2_CohFrictMat_CohFrictMat_CohFrictPhys.cpp
L libIp2_CohFrictMat_CohFrictMat_CohFrictPhys.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libIp2_CohFrictMat_CohFrictMat_CohFrictPhys.so
C pkg/dem/ConcretePM.cpp
C pkg/dem/CundallStrack.cpp
L libCundallStrack.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCundallStrack.so
C pkg/common/Cylinder.cpp
L libCylinder.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCylinder.so
C pkg/dem/Dem3DofGeom_FacetSphere.cpp
C pkg/dem/Dem3DofGeom_SphereSphere.cpp
L libDem3DofGeom_SphereSphere.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libDem3DofGeom_SphereSphere.so
L libDem3DofGeom_FacetSphere.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libDem3DofGeom_FacetSphere.so
C pkg/dem/Dem3DofGeom_WallSphere.cpp
C pkg/common/Wall.cpp
L libWall.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libWall.so
L libDem3DofGeom_WallSphere.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libDem3DofGeom_WallSphere.so
C pkg/dem/Disp2DPropLoadEngine.cpp
L libDisp2DPropLoadEngine.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libDisp2DPropLoadEngine.so
C pkg/dem/DomainLimiter.cpp
pkg/dem/DomainLimiter.cpp: In member function 'virtual void LawTester::action()':
pkg/dem/DomainLimiter.cpp:218: warning: comparison between signed and unsigned integer expressions
C pkg/dem/L3Geom.cpp
L libL3Geom.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libL3Geom.so
C pkg/dem/FacetTopologyAnalyzer.cpp
L libFacetTopologyAnalyzer.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libFacetTopologyAnalyzer.so
C pkg/dem/FlatGridCollider.cpp
L libFlatGridCollider.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libFlatGridCollider.so
C pkg/dem/FlowEngine.cpp
L libFlowEngine.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libFlowEngine.so
C pkg/common/ForceEngine.cpp
C pkg/dem/ForceTorqueRecorder.cpp
^FL libForceTorqueRecorder.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libForceTorqueRecorder.so
C pkg/common/Gl1_Aabb.cpp
L libGl1_Aabb.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGl1_Aabb.so
C pkg/common/Gl1_Box.cpp
L libGl1_Box.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGl1_Box.so
C pkg/common/Gl1_Facet.cpp
L libGl1_Facet.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGl1_Facet.so
C pkg/common/Gl1_Sphere.cpp
L libGl1_Sphere.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGl1_Sphere.so
C pkg/dem/HertzMindlin.cpp
In file included from /usr/include/boost/python/object/function_handle.hpp:10,
                 from /usr/include/boost/python/converter/arg_to_python.hpp:19,
                 from /usr/include/boost/python/call.hpp:15,
                 from /usr/include/boost/python/object_core.hpp:12,
                 from /usr/include/boost/python/args.hpp:25,
                 from /usr/include/boost/python.hpp:11,
                 from /home/dmaionchi/build-bzr2880/include/yade/lib/serialization/Serializable.hpp:23,
                 from /home/dmaionchi/build-bzr2880/include/yade/core/IPhys.hpp:12,
                 from /home/dmaionchi/build-bzr2880/include/yade/pkg/common/NormShearPhys.hpp:5,
                 from /home/dmaionchi/build-bzr2880/include/yade/pkg/dem/FrictPhys.hpp:10,
                 from pkg/dem/HertzMindlin.hpp:13,
                 from pkg/dem/HertzMindlin.cpp:4:
/home/dmaionchi/build-bzr2880/include/yade/lib/base/openmp-accu.hpp: In member function 'PyObject* boost::python::objects::caller_py_function_impl<Caller>::operator()(PyObject*, PyObject*) [with Caller = boost::python::detail::caller<boost::python::detail::member<OpenMPAccumulator<double>, Law2_ScGeom_MindlinPhys_Mindlin>, boost::python::default_call_policies, boost::mpl::vector3<void, Law2_ScGeom_MindlinPhys_Mindlin&, const OpenMPAccumulator<double>&> >]':
/home/dmaionchi/build-bzr2880/include/yade/lib/base/openmp-accu.hpp:100: warning: dereferencing pointer 'p.14309' does break strict-aliasing rules
/usr/include/boost/python/detail/destroy.hpp:90: note: initialized from here
/home/dmaionchi/build-bzr2880/include/yade/lib/base/openmp-accu.hpp:100: warning: dereferencing pointer 'p.14309' does break strict-aliasing rules
/usr/include/boost/python/detail/destroy.hpp:90: note: initialized from here
/home/dmaionchi/build-bzr2880/include/yade/lib/base/openmp-accu.hpp: In member function 'PyObject* boost::python::objects::caller_py_function_impl<Caller>::operator()(PyObject*, PyObject*) [with Caller = boost::python::detail::caller<boost::python::detail::member<OpenMPAccumulator<double>, Law2_ScGeom_MindlinPhys_Mindlin>, boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, boost::mpl::vector3<void, Law2_ScGeom_MindlinPhys_Mindlin&, const OpenMPAccumulator<double>&> >]':
/home/dmaionchi/build-bzr2880/include/yade/lib/base/openmp-accu.hpp:100: warning: dereferencing pointer 'p.14309' does break strict-aliasing rules
/usr/include/boost/python/detail/destroy.hpp:90: note: initialized from here
/home/dmaionchi/build-bzr2880/include/yade/lib/base/openmp-accu.hpp:100: warning: dereferencing pointer 'p.14309' does break strict-aliasing rules
/usr/include/boost/python/detail/destroy.hpp:90: note: initialized from here
/home/dmaionchi/build-bzr2880/include/yade/lib/base/openmp-accu.hpp: In member function 'PyObject* boost::python::objects::caller_py_function_impl<Caller>::operator()(PyObject*, PyObject*) [with Caller = boost::python::detail::caller<void (*)(Law2_ScGeom_MindlinPhys_Mindlin&, const OpenMPAccumulator<double>&), boost::python::default_call_policies, boost::mpl::vector3<void, Law2_ScGeom_MindlinPhys_Mindlin&, const OpenMPAccumulator<double>&> >]':
/home/dmaionchi/build-bzr2880/include/yade/lib/base/openmp-accu.hpp:100: warning: dereferencing pointer 'p.14309' does break strict-aliasing rules
/usr/include/boost/python/detail/destroy.hpp:90: note: initialized from here
/home/dmaionchi/build-bzr2880/include/yade/lib/base/openmp-accu.hpp:100: warning: dereferencing pointer 'p.14309' does break strict-aliasing rules
/usr/include/boost/python/detail/destroy.hpp:90: note: initialized from here
L libHertzMindlin.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libHertzMindlin.so
C pkg/dem/Ig2_Facet_Sphere_ScGeom.cpp
L libIg2_Facet_Sphere_ScGeom.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libIg2_Facet_Sphere_ScGeom.so
C pkg/dem/Ip2_2xNormalInelasticMat_NormalInelasticityPhys.cpp
C pkg/dem/NormalInelasticityPhys.cpp
L libNormalInelasticityPhys.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libNormalInelasticityPhys.so
C pkg/dem/NormalInelasticMat.cpp
L libNormalInelasticMat.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libNormalInelasticMat.so
L libIp2_2xNormalInelasticMat_NormalInelasticityPhys.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libIp2_2xNormalInelasticMat_NormalInelasticityPhys.so
C pkg/dem/KinemCNDEngine.cpp
C pkg/dem/KinemSimpleShearBox.cpp
L libKinemSimpleShearBox.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libKinemSimpleShearBox.so
L libKinemCNDEngine.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libKinemCNDEngine.so
C pkg/dem/KinemCNLEngine.cpp
L libKinemCNLEngine.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libKinemCNLEngine.so
C pkg/dem/KinemCNSEngine.cpp
L libKinemCNSEngine.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libKinemCNSEngine.so
C pkg/dem/KinemCTDEngine.cpp
L libKinemCTDEngine.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libKinemCTDEngine.so
C pkg/common/KinematicEngines.cpp
C pkg/dem/MicroMacroAnalyser.cpp
L libMicroMacroAnalyser.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libMicroMacroAnalyser.so
C pkg/dem/NormalInelasticityLaw.cpp
L libNormalInelasticityLaw.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libNormalInelasticityLaw.so
C pkg/common/ParallelEngine.cpp
L libParallelEngine.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libParallelEngine.so
C pkg/dem/ParticleSizeDistrbutionRPMRecorder.cpp
C pkg/dem/PeriIsoCompressor.cpp
C pkg/common/PersistentTriangulationCollider.cpp
L libPersistentTriangulationCollider.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libPersistentTriangulationCollider.so
C pkg/common/PyRunner.cpp
L libPyRunner.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libPyRunner.so
C pkg/common/ResetRandomPosition.cpp
L libResetRandomPosition.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libResetRandomPosition.so
C pkg/dem/STLImporter.cpp
C pkg/dem/SampleCapillaryPressureEngine.cpp
C pkg/dem/SimpleShear.cpp
L libSimpleShear.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libSimpleShear.so
C pkg/common/SpatialQuickSortCollider.cpp
L libSpatialQuickSortCollider.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libSpatialQuickSortCollider.so
C pkg/dem/SpherePack.cpp
/usr/include/eigen2/Eigen/src/Core/MathFunctions.h: In member function 'long int SpherePack::particleSD_2d(Vector2r, Vector2r, Real, bool, std::string, int, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, bool, int)':
/usr/include/eigen2/Eigen/src/Core/MathFunctions.h:137: warning: 'dr.Eigen::Matrix<double, 3, 1, 2, 3, 1>::m_storage.Eigen::ei_matrix_storage<double, 3, 3, 1, 2>::m_data.Eigen::ei_matrix_array<double, 3, 2, false>::array[2ul]' may be used uninitialized in this function
pkg/dem/SpherePack.cpp:392: note: 'dr.Eigen::Matrix<double, 3, 1, 2, 3, 1>::m_storage.Eigen::ei_matrix_storage<double, 3, 3, 1, 2>::m_data.Eigen::ei_matrix_array<double, 3, 2, false>::array[2ul]' was declared here
C pkg/dem/SpheresFactory.cpp
L libSpheresFactory.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libSpheresFactory.so
C pkg/common/StepDisplacer.cpp
L libStepDisplacer.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libStepDisplacer.so
C pkg/common/SubdomainBalancer.cpp
L libSubdomainBalancer.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libSubdomainBalancer.so
C pkg/dem/TesselationWrapper.cpp
L libTesselationWrapper.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libTesselationWrapper.so
C pkg/dem/ThreeDTriaxialEngine.cpp
C pkg/common/TorqueEngine.cpp
L libTorqueEngine.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libTorqueEngine.so
C pkg/dem/TriaxialTest.cpp
C pkg/dem/UnbalancedForceCallbacks.cpp
L libUnbalancedForceCallbacks.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libUnbalancedForceCallbacks.so
C pkg/dem/UniaxialStrainer.cpp
C pkg/dem/VTKRecorder.cpp
In file included from /usr/include/c++/4.4/backward/strstream:47,
                 from /usr/include/vtk-5.4/vtkIOStream.h:112,
                 from /usr/include/vtk-5.4/vtkSystemIncludes.h:40,
                 from /usr/include/vtk-5.4/vtkIndent.h:24,
                 from /usr/include/vtk-5.4/vtkObjectBase.h:43,
                 from /usr/include/vtk-5.4/vtkObject.h:41,
                 from /usr/include/vtk-5.4/vtkCellArray.h:35,
                 from pkg/dem/VTKRecorder.cpp:7:
/usr/include/c++/4.4/backward/backward_warning.h:28: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
C pkg/dem/WirePM.cpp
L libWirePM.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libWirePM.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/gts/__init__.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/gts/pygts.py
C py/mathWrap/miniEigen.cpp
L miniEigen.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/miniEigen.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/mtTkinter.py
C py/WeightedAverage2d.cpp
L WeightedAverage2d.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/WeightedAverage2d.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/__init__.py
C py/wrapper/customConverters.cpp
L _customConverters.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/_customConverters.so
C py/_eudoxos.cpp
In file included from /usr/include/c++/4.4/backward/strstream:47,
                 from /usr/include/vtk-5.4/vtkIOStream.h:112,
                 from /usr/include/vtk-5.4/vtkSystemIncludes.h:40,
                 from /usr/include/vtk-5.4/vtkIndent.h:24,
                 from /usr/include/vtk-5.4/vtkObjectBase.h:43,
                 from /usr/include/vtk-5.4/vtkObject.h:41,
                 from /usr/include/vtk-5.4/vtkLocator.h:53,
                 from /usr/include/vtk-5.4/vtkAbstractPointLocator.h:27,
                 from /usr/include/vtk-5.4/vtkPointLocator.h:39,
                 from py/_eudoxos.cpp:13:
/usr/include/c++/4.4/backward/backward_warning.h:28: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/_extraDocs.py
C py/pack/_packObb.cpp
L _packObb.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/_packObb.so
C py/pack/_packPredicates.cpp
L _packPredicates.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/_packPredicates.so
C py/pack/_packSpheres.cpp
C py/_utils.cpp
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/bodiesHandling.py
C core/main/pyboot.cpp
L boot.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/boot.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/config.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/eudoxos.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/export.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/geom.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/linterpolation.py
C py/log.cpp
L log.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/log.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/manpage.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/pack.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/params.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/plot.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/post2d.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/qt/Inspector.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/qt/SerializableEditor.py
C gui/qt4/GLViewer.cpp
C gui/qt4/OpenGLManager.cpp
C gui/qt4/_GLViewer.cpp
/usr/share/qt4/bin/moc -DQT_GUI_LIB -DQT_CORE_LIB -DQT_XML_LIB -DQT_OPENGL_LIB -DQT_SHARED -DPYGTS_HAS_NUMPY -DYADE_GTS -DYADE_LOG4CXX -DYADE_OPENGL -DYADE_OPENMP -DYADE_QT4 -DYADE_VTK -DYADE_OPENMP -DYADE_CAST=static_cast -DYADE_PTR_CAST=static_pointer_cast -DNDEBUG -I/usr/include/vtk-5.0 -I/usr/include/vtk-5.2 -I/usr/include/vtk-5.4 -I/usr/include/vtk-5.6 -I/usr/include/vtk -I/usr/include/eigen2 -I/home/dmaionchi/build-bzr2880/include -Iinclude -I/usr/include/python2.6 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtXml -I/usr/include/qt4/QtOpenGL -o /home/dmaionchi/build-bzr2880/gui/qt4/moc_GLViewer.cc gui/qt4/GLViewer.hpp
C /home/dmaionchi/build-bzr2880/gui/qt4/moc_GLViewer.cc
/usr/share/qt4/bin/moc -DQT_GUI_LIB -DQT_CORE_LIB -DQT_XML_LIB -DQT_OPENGL_LIB -DQT_SHARED -DPYGTS_HAS_NUMPY -DYADE_GTS -DYADE_LOG4CXX -DYADE_OPENGL -DYADE_OPENMP -DYADE_QT4 -DYADE_VTK -DYADE_OPENMP -DYADE_CAST=static_cast -DYADE_PTR_CAST=static_pointer_cast -DNDEBUG -I/usr/include/vtk-5.0 -I/usr/include/vtk-5.2 -I/usr/include/vtk-5.4 -I/usr/include/vtk-5.6 -I/usr/include/vtk -I/usr/include/eigen2 -I/home/dmaionchi/build-bzr2880/include -Iinclude -I/usr/include/python2.6 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtXml -I/usr/include/qt4/QtOpenGL -o /home/dmaionchi/build-bzr2880/gui/qt4/moc_OpenGLManager.cc gui/qt4/OpenGLManager.hpp
C /home/dmaionchi/build-bzr2880/gui/qt4/moc_OpenGLManager.cc
L _GLViewer.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/qt/_GLViewer.so
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/qt/__init__.py
pyrcc4 -o /home/dmaionchi/build-bzr2880/gui/qt4/img_rc.py gui/qt4/img.qrc
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/qt/img_rc.py
pyuic4 -o /home/dmaionchi/build-bzr2880/gui/qt4/ui_controller.py gui/qt4/controller.ui
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/qt/ui_controller.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/remote.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/runtime.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/system.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/__init__.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkList.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkTestDummy.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkTestNormalInelasticity.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkTestTriax.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/checkWeight.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/data/WallStressesCheckTest
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/checks/data/checkTestTriax.spheres
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/clump.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/cohesive-chain.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/core.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/engines.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/pbc.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/tests/wrapper.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/timing.py
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/utils.py
C py/wrapper/yadeWrapper.cpp
> /home/dmaionchi/YADE/lib/yade-bzr2880/py/yade/ymport.py
scons: done building targets.

scons: *** Found dependency cycle(s):
  Internal Error: no cycle found for node /home/dmaionchi/build-bzr2880/libTriaxialCompressionEngine.so (<SCons.Node.FS.File object at 0x5111b50>) in state pending
  /home/dmaionchi/build-bzr2880/libGl1_NormPhys.so -> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGl1_NormPhys.so -> /home/dmaionchi/build-bzr2880/libShop.so -> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libShop.so -> /home/dmaionchi/build-bzr2880/libGl1_NormPhys.so
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/py (<SCons.Node.FS.Dir object at 0x5a607d0>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/plugins (<SCons.Node.FS.Dir object at 0x295cc10>) in state pending
  /home/dmaionchi/build-bzr2880/libShop.so -> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libShop.so -> /home/dmaionchi/build-bzr2880/libGl1_NormPhys.so -> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGl1_NormPhys.so -> /home/dmaionchi/build-bzr2880/libShop.so
  /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libShop.so -> /home/dmaionchi/build-bzr2880/libGl1_NormPhys.so -> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libGl1_NormPhys.so -> /home/dmaionchi/build-bzr2880/libShop.so -> /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libShop.so
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libTriaxialCompressionEngine.so (<SCons.Node.FS.File object at 0x5127690>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/build-bzr2880/libRockPM.so (<SCons.Node.FS.File object at 0x3c74990>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libSpherePack.so (<SCons.Node.FS.File object at 0x5297f50>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libTriaxialStressController.so (<SCons.Node.FS.File object at 0x4c835d0>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libSTLImporter.so (<SCons.Node.FS.File object at 0x4d63950>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libRockPM.so (<SCons.Node.FS.File object at 0x3e96e50>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libConcretePM.so (<SCons.Node.FS.File object at 0x5074e50>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/build-bzr2880/libTriaxialStressController.so (<SCons.Node.FS.File object at 0x4befa90>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/build-bzr2880/libTriaxialStateRecorder.so (<SCons.Node.FS.File object at 0x569f350>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libCapillaryStressRecorder.so (<SCons.Node.FS.File object at 0x4bef690>) in state pending
  Internal Error: no cycle found for node /home/dmaionchi/YADE/lib/yade-bzr2880/plugins/libTriaxialStateRecorder.so (<SCons.Node.FS.File object at 0x5737290>) in state pending

File "/usr/lib/scons/SCons/Taskmaster.py", line 1011, in cleanup


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