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[Question #248457]: Problem with installing yade from source

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New question #248457 on Yade:
https://answers.launchpad.net/yade/+question/248457

Dear All,

I attempted to install yade from source.

The following results were got.

[  4%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/moc_OpenGLManager.cxx.o
Linking CXX shared library lib/x86_64-linux-gnu/_GLViewer.so
[  5%] Built target _GLViewer
Scanning dependencies of target yade
[  5%] Building CXX object CMakeFiles/yade.dir/core/Cell.cpp.o

[ 38%] Building CXX object CMakeFiles/yade.dir/pkg/dem/VTKRecorder.cpp.o
In file included from /usr/include/c++/4.8/backward/strstream:51:0,
                 from /usr/include/vtk-5.8/vtkIOStream.h:112,
                 from /usr/include/vtk-5.8/vtkSystemIncludes.h:40,
                 from /usr/include/vtk-5.8/vtkIndent.h:24,
                 from /usr/include/vtk-5.8/vtkObjectBase.h:43,
                 from /usr/include/vtk-5.8/vtkObject.h:41,
                 from /usr/include/vtk-5.8/vtkCell.h:40,
                 from /usr/include/vtk-5.8/vtkQuad.h:25,
                 from /home/jiadun/myYade/trunk/trunk-1.07.0/pkg/dem/VTKRecorder.hpp:3,
                 from /home/jiadun/myYade/trunk/trunk-1.07.0/pkg/dem/VTKRecorder.cpp:3:
/usr/include/c++/4.8/backward/backward_warning.h:32:2: 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. [-Wcpp]
 #warning \
[ 38%] Building CXX object CMakeFiles/yade.dir/pkg/dem/LudingPM.cpp.o

[ 51%] Building CXX object CMakeFiles/yade.dir/pkg/dem/FlowEngine.cpp.o
In file included from /home/jiadun/myYade/trunk/trunk-1.07.0/pkg/dem/FlowEngine.cpp:28:0:
/home/jiadun/myYade/trunk/trunk-1.07.0/pkg/dem/FlowEngine.hpp: In member function ‘void FlowEngine::cholmodStats()’:
/home/jiadun/myYade/trunk/trunk-1.07.0/pkg/dem/FlowEngine.hpp:199:91: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
      cerr << cholmod_print_common("PFV Cholmod factorization",&(solver->eSolver.cholmod()))<<endl;
                                                                                           ^
[ 52%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity.cpp.o

[ 61%] Building CXX object CMakeFiles/yade.dir/pkg/dem/STLImporter.cpp.o
In file included from /home/jiadun/myYade/trunk/trunk-1.07.0/pkg/dem/STLImporter.cpp:10:0:
/home/jiadun/myYade/build/yade/lib/import/STLReader.hpp: In member function ‘bool STLReader::open_ascii(const char*, OutV, OutE, OutF, OutN) [with OutV = std::back_insert_iterator<std::vector<double> >; OutE = std::back_insert_iterator<std::vector<int> >; OutF = std::back_insert_iterator<std::vector<int> >; OutN = std::back_insert_iterator<std::vector<double> >]’:
/home/jiadun/myYade/build/yade/lib/import/STLReader.hpp:120:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %*s %f %f %f\n", &n[0], &n[1], &n[2]);
  ^
/home/jiadun/myYade/build/yade/lib/import/STLReader.hpp:121:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %*s");
  ^
/home/jiadun/myYade/build/yade/lib/import/STLReader.hpp:122:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %f %f %f\n", &v[0][0],  &v[0][1],  &v[0][2]);
  ^
/home/jiadun/myYade/build/yade/lib/import/STLReader.hpp:123:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %f %f %f\n", &v[1][0],  &v[1][1],  &v[1][2]);
  ^
/home/jiadun/myYade/build/yade/lib/import/STLReader.hpp:124:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %f %f %f\n", &v[2][0],  &v[2][1],  &v[2][2]);
  ^
/home/jiadun/myYade/build/yade/lib/import/STLReader.hpp:125:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s"); // end loop
  ^
/home/jiadun/myYade/build/yade/lib/import/STLReader.hpp:126:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s"); // end facet
  ^
[ 62%] Building CXX object CMakeFiles/yade.dir/pkg/common/PyRunner.cpp.o

[ 95%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/TriaxialState.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/libyade.so
[ 95%] Built target yade
Scanning dependencies of target boot
[ 95%] Building CXX object CMakeFiles/boot.dir/core/main/pyboot.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/boot.so
[ 95%] Built target boot
Scanning dependencies of target WeightedAverage2d
[ 95%] Building CXX object py/CMakeFiles/WeightedAverage2d.dir/WeightedAverage2d.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/WeightedAverage2d.so
[ 95%] Built target WeightedAverage2d
Scanning dependencies of target _customConverters
[ 96%] Building CXX object py/CMakeFiles/_customConverters.dir/wrapper/customConverters.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/_customConverters.so
[ 96%] Built target _customConverters
Scanning dependencies of target _packObb
[ 96%] Building CXX object py/CMakeFiles/_packObb.dir/pack/_packObb.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/_packObb.so
[ 96%] Built target _packObb
Scanning dependencies of target _packPredicates
[ 97%] Building CXX object py/CMakeFiles/_packPredicates.dir/pack/_packPredicates.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/_packPredicates.so
[ 97%] Built target _packPredicates
Scanning dependencies of target _packSpheres
[ 98%] Building CXX object py/CMakeFiles/_packSpheres.dir/pack/_packSpheres.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/_packSpheres.so
[ 98%] Built target _packSpheres
Scanning dependencies of target _polyhedra_utils
[ 98%] Building CXX object py/CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils.cpp.o
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/jiadun/myYade/trunk/trunk-1.07.0/py/_polyhedra_utils.cpp:17:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
Linking CXX shared library lib/x86_64-linux-gnu/_polyhedra_utils.so
[ 98%] Built target _polyhedra_utils
Scanning dependencies of target _utils
[ 99%] Building CXX object py/CMakeFiles/_utils.dir/_utils.cpp.o
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/jiadun/myYade/trunk/trunk-1.07.0/py/_utils.cpp:18:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
Linking CXX shared library lib/x86_64-linux-gnu/_utils.so
[ 99%] Built target _utils
Scanning dependencies of target wrapper
[100%] Building CXX object py/CMakeFiles/wrapper.dir/wrapper/yadeWrapper.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/wrapper.so
[100%] Built target wrapper

make doc
Scanning dependencies of target doc
Welcome to Yade 1.07.0 
TCP python prompt on localhost:9000, auth cookie `sdacyk'
XMLRPC info provider on http://localhost:21000
Running script yadeSphinx.py
Running Sphinx v1.2.2

Exception occurred:
  File "/home/jiadun/myYade/build/doc/sphinx/ipython_directive.py", line 83, in <module>
    from IPython.Shell import MatplotlibShell
ImportError: No module named Shell
The full traceback has been saved in /tmp/sphinx-err-6ZrDDH.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!
Traceback (most recent call last):
  File "/home/jiadun/myYade/trunk/install/bin/yade-1.07.0", line 178, in runScript
    execfile(script,globals())
  File "yadeSphinx.py", line 222, in <module>
    makeBaseClassesClickable((outDir+'/html/yade.wrapper.html'),writer)
  File "yadeSphinx.py", line 154, in makeBaseClassesClickable
    for l in open(f):
IOError: [Errno 2] No such file or directory: '_build/html/yade.wrapper.html'
Traceback (most recent call last):
  File "/home/jiadun/myYade/trunk/install/bin/yade-1.07.0", line 273, in <module>
    userSession(qt4=True,qapp=qapp)
  File "/home/jiadun/myYade/trunk/install/bin/yade-1.07.0", line 208, in userSession
    from IPython.Shell import IPShellEmbed
ImportError: No module named Shell
make[3]: *** [doc] Error 1
make[2]: *** [CMakeFiles/doc.dir/all] Error 2
make[1]: *** [CMakeFiles/doc.dir/rule] Error 2
make: *** [doc] Error 2

jiadun@jiadun-Lenovo-IdeaPad-Z500:~/myYade/trunk/install/bin$ ./yade-1.07.0
Welcome to Yade 1.07.0 
TCP python prompt on localhost:9000, auth cookie `cysaek'
XMLRPC info provider on http://localhost:21000
Traceback (most recent call last):
  File "./yade-1.07.0", line 273, in <module>
    userSession(qt4=True,qapp=qapp)
  File "./yade-1.07.0", line 208, in userSession
    from IPython.Shell import IPShellEmbed
ImportError: No module named Shell

Best regards,
Jiadun

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