[  0%] Copying Resource files
[  0%] Built target copy-external-files
[  2%] Built target CIPUtilities
[  2%] Built target generateChestConventions
[  8%] Built target CIPCommon
[  9%] Built target CIPIO
running build_ext
skipping '/.../cip_python/utils/gco_python/gco_python.cpp' Cython extension (up-to-date)
building 'pygco' extension
/usr/bin/cc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/.../Utilities/GraphCutsOptimization -I/root/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/root/miniconda2/include/python2.7 -c /.../cip_python/utils/gco_python/gco_python.cpp -o build/temp.linux-x86_64-2.7/.../cip_python/utils/gco_python/gco_python.o

cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++

In file included from /root/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
                 from /root/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /root/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /.../cip_python/utils/gco_python/gco_python.cpp:449:

/root/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
/usr/bin/cc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/.../Utilities/GraphCutsOptimization -I/root/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/root/miniconda2/include/python2.7 -c /.../Utilities/GraphCutsOptimization/GCoptimization.cpp -o build/temp.linux-x86_64-2.7/.../Utilities/GraphCutsOptimization/GCoptimization.o

cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++

In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:
/.../Utilities/GraphCutsOptimization/GCoptimization.h: In constructor 'GCoptimization::GCoptimization(GCoptimization::SiteID, GCoptimization::LabelID)':

/.../Utilities/GraphCutsOptimization/GCoptimization.h:311:10: warning: 'GCoptimization::m_smoothcostFn' will be initialized after [-Wreorder]

  void*   m_smoothcostFn;
          ^~~~~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:310:10: warning:   'void* GCoptimization::m_datacostFn' [-Wreorder]

  void*   m_datacostFn;
          ^~~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:

/.../Utilities/GraphCutsOptimization/GCoptimization.h:321:86: warning: 'GCoptimization::m_setupDataCostsSwap' will be initialized after [-Wreorder]

  void (GCoptimization::*m_setupDataCostsSwap)(SiteID,LabelID,LabelID,EnergyT*,SiteID*);
                                                                                      ^

/.../Utilities/GraphCutsOptimization/GCoptimization.h:319:83: warning:   'void (GCoptimization::* GCoptimization::m_setupDataCostsExpansion)(GCoptimization::SiteID, GCoptimization::LabelID, GCoptimization::EnergyT*, GCoptimization::SiteID*)' [-Wreorder]

  void (GCoptimization::*m_setupDataCostsExpansion)(SiteID,LabelID,EnergyT*,SiteID*);
                                                                                   ^

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:

/.../Utilities/GraphCutsOptimization/GCoptimization.h:322:88: warning: 'GCoptimization::m_setupSmoothCostsSwap' will be initialized after [-Wreorder]

  void (GCoptimization::*m_setupSmoothCostsSwap)(SiteID,LabelID,LabelID,EnergyT*,SiteID*);
                                                                                        ^

/.../Utilities/GraphCutsOptimization/GCoptimization.h:320:85: warning:   'void (GCoptimization::* GCoptimization::m_setupSmoothCostsExpansion)(GCoptimization::SiteID, GCoptimization::LabelID, GCoptimization::EnergyT*, GCoptimization::SiteID*)' [-Wreorder]

  void (GCoptimization::*m_setupSmoothCostsExpansion)(SiteID,LabelID,EnergyT*,SiteID*);
                                                                                     ^

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:

/.../Utilities/GraphCutsOptimization/GCoptimization.h:324:52: warning: 'GCoptimization::m_updateLabelingDataCosts' will be initialized after [-Wreorder]

  void (GCoptimization::*m_updateLabelingDataCosts)();
                                                    ^

/.../Utilities/GraphCutsOptimization/GCoptimization.h:317:59: warning:   'GCoptimization::EnergyType (GCoptimization::* GCoptimization::m_giveSmoothEnergyInternal)()' [-Wreorder]

  EnergyType (GCoptimization::*m_giveSmoothEnergyInternal)();
                                                           ^

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:

/.../Utilities/GraphCutsOptimization/GCoptimization.h:328:57: warning: 'GCoptimization::m_solveSpecialCases' will be initialized after [-Wreorder]

  bool (GCoptimization::*m_solveSpecialCases)(EnergyType&);
                                                         ^

/.../Utilities/GraphCutsOptimization/GCoptimization.h:326:36: warning:   'void (* GCoptimization::m_datacostFnDelete)(void*)' [-Wreorder]

  void (*m_datacostFnDelete)(void* f);
                                    ^

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:

/.../Utilities/GraphCutsOptimization/GCoptimization.h:327:38: warning: 'GCoptimization::m_smoothcostFnDelete' will be initialized after [-Wreorder]

  void (*m_smoothcostFnDelete)(void* f);
                                      ^

/.../Utilities/GraphCutsOptimization/GCoptimization.h:298:11: warning:   'int GCoptimization::m_random_label_order' [-Wreorder]

  int      m_random_label_order;
           ^~~~~~~~~~~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:

/.../Utilities/GraphCutsOptimization/GCoptimization.h:308:18: warning: 'GCoptimization::m_verbosity' will be initialized after [-Wreorder]

  int             m_verbosity;
                  ^~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:307:18: warning:   'bool GCoptimization::m_labelingInfoDirty' [-Wreorder]

  bool            m_labelingInfoDirty;
                  ^~~~~~~~~~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:

/.../Utilities/GraphCutsOptimization/GCoptimization.h:307:18: warning: 'GCoptimization::m_labelingInfoDirty' will be initialized after [-Wreorder]

  bool            m_labelingInfoDirty;
                  ^~~~~~~~~~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:293:11: warning:   'GCoptimization::SiteID* GCoptimization::m_lookupSiteVar' [-Wreorder]

  SiteID  *m_lookupSiteVar; // holds index of variable corresponding to site participating in a move,
           ^~~~~~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:

/.../Utilities/GraphCutsOptimization/GCoptimization.h:293:11: warning: 'GCoptimization::m_lookupSiteVar' will be initialized after [-Wreorder]

  SiteID  *m_lookupSiteVar; // holds index of variable corresponding to site participating in a move,
           ^~~~~~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:292:11: warning:   'GCoptimization::LabelID* GCoptimization::m_labeling' [-Wreorder]

  LabelID *m_labeling;
           ^~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:

/.../Utilities/GraphCutsOptimization/GCoptimization.h:303:18: warning: 'GCoptimization::m_activeLabelCounts' will be initialized after [-Wreorder]

  SiteID*         m_activeLabelCounts;
                  ^~~~~~~~~~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:296:11: warning:   'int GCoptimization::m_stepsThisCycle' [-Wreorder]

  int      m_stepsThisCycle;
           ^~~~~~~~~~~~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:89:1: warning:   when initialized here [-Wreorder]

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^~~~~~~~~~~~~~
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp: In member function 'void GCoptimization::updateLabelingInfo(bool, bool, bool)':

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:1177:15: warning: unused variable 'energy' [-Wunused-variable]

    EnergyType energy = 0;
               ^~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:
/.../Utilities/GraphCutsOptimization/GCoptimization.h: In instantiation of 'GCoptimization::GreedyIter<DataCostT>::GreedyIter(DataCostT&, GCoptimization::SiteID) [with DataCostT = GCoptimization::DataCostFnFromArray; GCoptimization::SiteID = int]':
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:591:25:   required from 'GCoptimization::EnergyType GCoptimization::solveGreedy() [with DataCostT = GCoptimization::DataCostFnFromArray; GCoptimization::EnergyType = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:510:35:   required from 'bool GCoptimization::solveSpecialCases(GCoptimization::EnergyType&) [with DataCostT = GCoptimization::DataCostFnFromArray; GCoptimization::EnergyType = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:121:26:   required from here

/.../Utilities/GraphCutsOptimization/GCoptimization.h:520:14: warning: 'GCoptimization::GreedyIter<GCoptimization::DataCostFnFromArray>::m_dc' will be initialized after [-Wreorder]

   DataCostT& m_dc;
              ^~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:519:10: warning:   'GCoptimization::SiteID GCoptimization::GreedyIter<GCoptimization::DataCostFnFromArray>::m_site' [-Wreorder]

   SiteID m_site;
          ^~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:491:3: warning:   when initialized here [-Wreorder]

   GreedyIter(DataCostT& dc, SiteID numSites)
   ^~~~~~~~~~
/.../Utilities/GraphCutsOptimization/GCoptimization.h: In instantiation of 'GCoptimization::GreedyIter<DataCostT>::GreedyIter(DataCostT&, GCoptimization::SiteID) [with DataCostT = GCoptimization::DataCostFunctor; GCoptimization::SiteID = int]':
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:591:25:   required from 'GCoptimization::EnergyType GCoptimization::solveGreedy() [with DataCostT = GCoptimization::DataCostFunctor; GCoptimization::EnergyType = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:510:35:   required from 'bool GCoptimization::solveSpecialCases(GCoptimization::EnergyType&) [with DataCostT = GCoptimization::DataCostFunctor; GCoptimization::EnergyType = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:769:49:   required from here

/.../Utilities/GraphCutsOptimization/GCoptimization.h:520:14: warning: 'GCoptimization::GreedyIter<GCoptimization::DataCostFunctor>::m_dc' will be initialized after [-Wreorder]

   DataCostT& m_dc;
              ^~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:519:10: warning:   'GCoptimization::SiteID GCoptimization::GreedyIter<GCoptimization::DataCostFunctor>::m_site' [-Wreorder]

   SiteID m_site;
          ^~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:491:3: warning:   when initialized here [-Wreorder]

   GreedyIter(DataCostT& dc, SiteID numSites)
   ^~~~~~~~~~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.h:111:0,
                 from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:
/.../Utilities/GraphCutsOptimization/maxflow.cpp: In instantiation of 'void Graph<captype, tcaptype, flowtype>::process_sink_orphan(Graph<captype, tcaptype, flowtype>::node*) [with captype = int; tcaptype = int; flowtype = long long int]':
/.../Utilities/GraphCutsOptimization/maxflow.cpp:584:41:   required from 'flowtype Graph<captype, tcaptype, flowtype>::maxflow(bool, Block<int>*) [with captype = int; tcaptype = int; flowtype = long long int]'
/.../Utilities/GraphCutsOptimization/energy.h:325:32:   required from 'Energy<captype, tcaptype, flowtype>::TotalValue Energy<captype, tcaptype, flowtype>::minimize() [with captype = int; tcaptype = int; flowtype = long long int; Energy<captype, tcaptype, flowtype>::TotalValue = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:1241:37:   required from here

/.../Utilities/GraphCutsOptimization/maxflow.cpp:443:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]

  if (i->parent = a0_min)
  ^~
/.../Utilities/GraphCutsOptimization/maxflow.cpp: In instantiation of 'void Graph<captype, tcaptype, flowtype>::process_source_orphan(Graph<captype, tcaptype, flowtype>::node*) [with captype = int; tcaptype = int; flowtype = long long int]':
/.../Utilities/GraphCutsOptimization/maxflow.cpp:585:43:   required from 'flowtype Graph<captype, tcaptype, flowtype>::maxflow(bool, Block<int>*) [with captype = int; tcaptype = int; flowtype = long long int]'
/.../Utilities/GraphCutsOptimization/energy.h:325:32:   required from 'Energy<captype, tcaptype, flowtype>::TotalValue Energy<captype, tcaptype, flowtype>::minimize() [with captype = int; tcaptype = int; flowtype = long long int; Energy<captype, tcaptype, flowtype>::TotalValue = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:1241:37:   required from here

/.../Utilities/GraphCutsOptimization/maxflow.cpp:366:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]

  if (i->parent = a0_min)
  ^~
In file included from /.../Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:
/.../Utilities/GraphCutsOptimization/GCoptimization.h: In instantiation of 'GCoptimization::GreedyIter<DataCostT>::GreedyIter(DataCostT&, GCoptimization::SiteID) [with DataCostT = GCoptimization::DataCostFnFromFunction; GCoptimization::SiteID = int]':
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:591:25:   required from 'GCoptimization::EnergyType GCoptimization::solveGreedy() [with DataCostT = GCoptimization::DataCostFnFromFunction; GCoptimization::EnergyType = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:510:35:   required from 'bool GCoptimization::solveSpecialCases(GCoptimization::EnergyType&) [with DataCostT = GCoptimization::DataCostFnFromFunction; GCoptimization::EnergyType = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:235:30:   required from 'void GCoptimization::specializeDataCostFunctor(UserFunctor) [with UserFunctor = GCoptimization::DataCostFnFromFunction]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:717:54:   required from here

/.../Utilities/GraphCutsOptimization/GCoptimization.h:520:14: warning: 'GCoptimization::GreedyIter<GCoptimization::DataCostFnFromFunction>::m_dc' will be initialized after [-Wreorder]

   DataCostT& m_dc;
              ^~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:519:10: warning:   'GCoptimization::SiteID GCoptimization::GreedyIter<GCoptimization::DataCostFnFromFunction>::m_site' [-Wreorder]

   SiteID m_site;
          ^~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:491:3: warning:   when initialized here [-Wreorder]

   GreedyIter(DataCostT& dc, SiteID numSites)
   ^~~~~~~~~~
/.../Utilities/GraphCutsOptimization/GCoptimization.h: In instantiation of 'GCoptimization::GreedyIter<DataCostT>::GreedyIter(DataCostT&, GCoptimization::SiteID) [with DataCostT = GCoptimization::DataCostFnFromFunctionExtra; GCoptimization::SiteID = int]':
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:591:25:   required from 'GCoptimization::EnergyType GCoptimization::solveGreedy() [with DataCostT = GCoptimization::DataCostFnFromFunctionExtra; GCoptimization::EnergyType = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:510:35:   required from 'bool GCoptimization::solveSpecialCases(GCoptimization::EnergyType&) [with DataCostT = GCoptimization::DataCostFnFromFunctionExtra; GCoptimization::EnergyType = long long int]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:235:30:   required from 'void GCoptimization::specializeDataCostFunctor(UserFunctor) [with UserFunctor = GCoptimization::DataCostFnFromFunctionExtra]'
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:725:70:   required from here

/.../Utilities/GraphCutsOptimization/GCoptimization.h:520:14: warning: 'GCoptimization::GreedyIter<GCoptimization::DataCostFnFromFunctionExtra>::m_dc' will be initialized after [-Wreorder]

   DataCostT& m_dc;
              ^~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:519:10: warning:   'GCoptimization::SiteID GCoptimization::GreedyIter<GCoptimization::DataCostFnFromFunctionExtra>::m_site' [-Wreorder]

   SiteID m_site;
          ^~~~~~

/.../Utilities/GraphCutsOptimization/GCoptimization.h:491:3: warning:   when initialized here [-Wreorder]

   GreedyIter(DataCostT& dc, SiteID numSites)
   ^~~~~~~~~~
/.../Utilities/GraphCutsOptimization/GCoptimization.cpp: In member function 'void GCoptimizationGridGraph::computeNeighborWeights(GCoptimization::EnergyTermType*, GCoptimization::EnergyTermType*)':

/.../Utilities/GraphCutsOptimization/GCoptimization.cpp:1514:30: warning: 'weight' may be used uninitialized in this function [-Wmaybe-uninitialized]

    m_neighborsWeights[i*4+n] = weight;
    ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/usr/bin/cc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/.../Utilities/GraphCutsOptimization -I/root/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/root/miniconda2/include/python2.7 -c /.../Utilities/GraphCutsOptimization/graph.cpp -o build/temp.linux-x86_64-2.7/.../Utilities/GraphCutsOptimization/graph.o

cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++

/usr/bin/cc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/.../Utilities/GraphCutsOptimization -I/root/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/root/miniconda2/include/python2.7 -c /.../Utilities/GraphCutsOptimization/LinkedBlockList.cpp -o build/temp.linux-x86_64-2.7/.../Utilities/GraphCutsOptimization/LinkedBlockList.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
/.../Utilities/GraphCutsOptimization/LinkedBlockList.cpp: In member function 'void LinkedBlockList::addFront(ListType)':
/.../Utilities/GraphCutsOptimization/LinkedBlockList.cpp:18:35: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_head ->m_item[m_head_block_size] = item;
                                   ^
/.../Utilities/GraphCutsOptimization/LinkedBlockList.cpp: In member function 'void* LinkedBlockList::next()':
/.../Utilities/GraphCutsOptimization/LinkedBlockList.cpp:26:53: warning: array subscript has type 'char' [-Wchar-subscripts]
  ListType toReturn = m_cursor -> m_item[m_cursor_ind];
                                                     ^
The maximum number of reported warnings or errors has been reached!!!