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Current branch master is up to date.
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/cip/CIP-build/CIPPython-install already exists. Miniconda will not be installed
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Please update conda by running

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Requirement already satisfied: pyyaml in /home/ubuntu/.local/lib/python2.7/site-packages (from keras==2.0.8)
Requirement already satisfied: six>=1.9.0 in /home/ubuntu/.local/lib/python2.7/site-packages (from keras==2.0.8)
Requirement already satisfied: scipy>=0.14 in ./CIPPython-install/lib/python2.7/site-packages (from keras==2.0.8)
Requirement already satisfied: numpy>=1.9.1 in ./CIPPython-install/lib/python2.7/site-packages (from keras==2.0.8)
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You should consider upgrading via the 'pip install --upgrade pip' command.
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# All requested packages already installed.

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Please update conda by running

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Please update conda by running

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# All requested packages already installed.

[ 14%] Performing installnibabel step for 'CIPPython'
The directory '/home/ubuntu/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
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You are using pip version 9.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
[ 15%] Performing installnumpy step for 'CIPPython'
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Downloading and Extracting Packages
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# All requested packages already installed.

CMake Deprecation Warning at CMakeLists.txt:42 (cmake_policy):
  The OLD behavior for policy CMP0054 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.

CMake Warning (dev) at CMakeLists.txt:142 (find_package):

  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  CMake variable ZLIB_ROOT is set to:

    /cip/CIP-build/zlib-install

  For compatibility, CMake is ignoring the variable.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at CMakeLists.txt:555 (install):

  Policy CMP0062 is not set: Disallow install() of export() result.  Run
  "cmake --help-policy CMP0062" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The file

    /cip/CIP-build/teem-build/TeemLibraryDepends.cmake

  was generated by the export() command.  It should not be installed with the
  install() command.  Use the install(EXPORT) mechanism instead.  See the

CMake Deprecation Warning at Modules/ThirdParty/VNL/src/vxl/CMakeLists.txt:28 (cmake_policy):
  The OLD behavior for policy CMP0033 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.

CMake Warning (dev) at Modules/ThirdParty/VNL/src/vxl/config/cmake/Modules/FindZLIB.cmake:20 (find_package):

  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  CMake variable ZLIB_ROOT is set to:

    /cip/CIP-build/zlib-install

  For compatibility, CMake is ignoring the variable.
Call Stack (most recent call first):

  Modules/ThirdParty/VNL/src/vxl/v3p/CMakeLists.txt:19 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Performing Test ITK_PRIVATE_DYNAMIC_CAST - Success

CMake Warning (dev) at Modules/ThirdParty/ZLIB/CMakeLists.txt:8 (find_package):

  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  CMake variable ZLIB_ROOT is set to:

    /cip/CIP-build/zlib-install

  For compatibility, CMake is ignoring the variable.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found ZLIB: /cip/CIP-build/zlib-install/lib/libzlib.a (found version "1.2.3") 

CMake Warning (dev) at Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt:401 (find_package):

  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  CMake variable ZLIB_ROOT is set to:

    /cip/CIP-build/zlib-install

  For compatibility, CMake is ignoring the variable.
This warning is for project developers.  Use -Wno-dev to suppress it.

[  3%] Building CXX object Common/CMakeFiles/CIPCommon.dir/cipLeftLobesThinPlateSplineSurfaceModelToParticlesMetric.cxx.o
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/cip/CIP/Common/cipGeometryTopologyData.cxx: In member function ‘cip::GeometryTopologyData::BOUNDINGBOX* cip::GeometryTopologyData::InsertBoundingBox(unsigned char, unsigned char, unsigned char, cip::GeometryTopologyData::StartType, cip::GeometryTopologyData::SizeType, std::__cxx11::string)’:

/cip/CIP/Common/cipGeometryTopologyData.cxx:104:15: warning: address of local variable ‘bb’ returned [-Wreturn-local-addr]

   BOUNDINGBOX bb;
               ^
/cip/CIP/Common/cipGeometryTopologyData.cxx: In member function ‘cip::GeometryTopologyData::BOUNDINGBOX* cip::GeometryTopologyData::InsertBoundingBox(int, unsigned char, unsigned char, unsigned char, cip::GeometryTopologyData::StartType, cip::GeometryTopologyData::SizeType, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)’:

/cip/CIP/Common/cipGeometryTopologyData.cxx:157:15: warning: address of local variable ‘bb’ returned [-Wreturn-local-addr]

   BOUNDINGBOX bb;
               ^
/cip/CIP/Common/cipGeometryTopologyData.cxx: In member function ‘cip::GeometryTopologyData::POINT* cip::GeometryTopologyData::InsertPoint(unsigned char, unsigned char, unsigned char, cip::GeometryTopologyData::CoordinateType, std::__cxx11::string)’:

/cip/CIP/Common/cipGeometryTopologyData.cxx:231:9: warning: address of local variable ‘p’ returned [-Wreturn-local-addr]

   POINT p;
         ^
/cip/CIP/Common/cipGeometryTopologyData.cxx: In member function ‘cip::GeometryTopologyData::POINT* cip::GeometryTopologyData::InsertPoint(int, unsigned char, unsigned char, unsigned char, cip::GeometryTopologyData::CoordinateType, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)’:

/cip/CIP/Common/cipGeometryTopologyData.cxx:267:9: warning: address of local variable ‘p’ returned [-Wreturn-local-addr]

   POINT p;
         ^
[  5%] Building CXX object Common/CMakeFiles/CIPCommon.dir/vtkSimpleLungMask.cxx.o
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creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/cip
creating build/temp.linux-x86_64-2.7/cip/CIP
creating build/temp.linux-x86_64-2.7/cip/CIP/cip_python
creating build/temp.linux-x86_64-2.7/cip/CIP/cip_python/utils
creating build/temp.linux-x86_64-2.7/cip/CIP/cip_python/utils/gco_python
creating build/temp.linux-x86_64-2.7/cip/CIP/Utilities
creating build/temp.linux-x86_64-2.7/cip/CIP/Utilities/GraphCutsOptimization
/usr/bin/cc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/cip/CIP/Utilities/GraphCutsOptimization -I/cip/CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include -I/cip/CIP-build/CIPPython-install/include/python2.7 -c /cip/CIP/cip_python/utils/gco_python/gco_python.cpp -o build/temp.linux-x86_64-2.7/cip/CIP/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 /cip/CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:0,
                 from /cip/CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /cip/CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /cip/CIP/cip_python/utils/gco_python/gco_python.cpp:449:

/cip/CIP-build/CIPPython-install/lib/python2.7/site-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 " \
  ^
/usr/bin/cc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/cip/CIP/Utilities/GraphCutsOptimization -I/cip/CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include -I/cip/CIP-build/CIPPython-install/include/python2.7 -c /cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp -o build/temp.linux-x86_64-2.7/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.o

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:311:10: warning: ‘GCoptimization::m_smoothcostFn’ will be initialized after [-Wreorder]

  void*   m_smoothcostFn;
          ^

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:310:10: warning:   ‘void* GCoptimization::m_datacostFn’ [-Wreorder]

  void*   m_datacostFn;
          ^

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:321:86: warning: ‘GCoptimization::m_setupDataCostsSwap’ will be initialized after [-Wreorder]

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

/cip/CIP/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*);
                                                                                   ^

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:322:88: warning: ‘GCoptimization::m_setupSmoothCostsSwap’ will be initialized after [-Wreorder]

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

/cip/CIP/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*);
                                                                                     ^

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:324:52: warning: ‘GCoptimization::m_updateLabelingDataCosts’ will be initialized after [-Wreorder]

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:317:59: warning:   ‘GCoptimization::EnergyType (GCoptimization::* GCoptimization::m_giveSmoothEnergyInternal)()’ [-Wreorder]

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

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:328:57: warning: ‘GCoptimization::m_solveSpecialCases’ will be initialized after [-Wreorder]

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:326:36: warning:   ‘void (* GCoptimization::m_datacostFnDelete)(void*)’ [-Wreorder]

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

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:327:38: warning: ‘GCoptimization::m_smoothcostFnDelete’ will be initialized after [-Wreorder]

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:298:11: warning:   ‘int GCoptimization::m_random_label_order’ [-Wreorder]

  int      m_random_label_order;
           ^

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:308:18: warning: ‘GCoptimization::m_verbosity’ will be initialized after [-Wreorder]

  int             m_verbosity;
                  ^

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:307:18: warning:   ‘bool GCoptimization::m_labelingInfoDirty’ [-Wreorder]

  bool            m_labelingInfoDirty;
                  ^

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:307:18: warning: ‘GCoptimization::m_labelingInfoDirty’ will be initialized after [-Wreorder]

  bool            m_labelingInfoDirty;
                  ^

/cip/CIP/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,
           ^

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

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

/cip/CIP/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,
           ^

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:292:11: warning:   ‘GCoptimization::LabelID* GCoptimization::m_labeling’ [-Wreorder]

  LabelID *m_labeling;
           ^

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:303:18: warning: ‘GCoptimization::m_activeLabelCounts’ will be initialized after [-Wreorder]

  SiteID*         m_activeLabelCounts;
                  ^

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:296:11: warning:   ‘int GCoptimization::m_stepsThisCycle’ [-Wreorder]

  int      m_stepsThisCycle;
           ^

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

 GCoptimization::GCoptimization(SiteID nSites, LabelID nLabels) 
 ^
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp: In member function ‘void GCoptimization::updateLabelingInfo(bool, bool, bool)’:

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:1177:15: warning: unused variable ‘energy’ [-Wunused-variable]

    EnergyType energy = 0;
               ^
In file included from /cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h: In instantiation of ‘GCoptimization::GreedyIter<DataCostT>::GreedyIter(DataCostT&, GCoptimization::SiteID) [with DataCostT = GCoptimization::DataCostFnFromArray; GCoptimization::SiteID = int]’:
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:591:45:   required from ‘GCoptimization::EnergyType GCoptimization::solveGreedy() [with DataCostT = GCoptimization::DataCostFnFromArray; GCoptimization::EnergyType = long long int]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:510:35:   required from ‘bool GCoptimization::solveSpecialCases(GCoptimization::EnergyType&) [with DataCostT = GCoptimization::DataCostFnFromArray; GCoptimization::EnergyType = long long int]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:121:26:   required from here

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

   DataCostT& m_dc;
              ^

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

   SiteID m_site;
          ^

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

   GreedyIter(DataCostT& dc, SiteID numSites)
   ^
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h: In instantiation of ‘GCoptimization::GreedyIter<DataCostT>::GreedyIter(DataCostT&, GCoptimization::SiteID) [with DataCostT = GCoptimization::DataCostFunctor; GCoptimization::SiteID = int]’:
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:591:45:   required from ‘GCoptimization::EnergyType GCoptimization::solveGreedy() [with DataCostT = GCoptimization::DataCostFunctor; GCoptimization::EnergyType = long long int]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:510:35:   required from ‘bool GCoptimization::solveSpecialCases(GCoptimization::EnergyType&) [with DataCostT = GCoptimization::DataCostFunctor; GCoptimization::EnergyType = long long int]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:769:30:   required from here

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

   DataCostT& m_dc;
              ^

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

   SiteID m_site;
          ^

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

   GreedyIter(DataCostT& dc, SiteID numSites)
   ^
In file included from /cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h:111:0,
                 from /cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:4:
/cip/CIP/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]’:
/cip/CIP/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]’
/cip/CIP/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]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:1241:37:   required from here

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

  if (i->parent = a0_min)
  ^
/cip/CIP/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]’:
/cip/CIP/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]’
/cip/CIP/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]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:1241:37:   required from here

/cip/CIP/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 /cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:4:0:
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h: In instantiation of ‘GCoptimization::GreedyIter<DataCostT>::GreedyIter(DataCostT&, GCoptimization::SiteID) [with DataCostT = GCoptimization::DataCostFnFromFunction; GCoptimization::SiteID = int]’:
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:591:45:   required from ‘GCoptimization::EnergyType GCoptimization::solveGreedy() [with DataCostT = GCoptimization::DataCostFnFromFunction; GCoptimization::EnergyType = long long int]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:510:35:   required from ‘bool GCoptimization::solveSpecialCases(GCoptimization::EnergyType&) [with DataCostT = GCoptimization::DataCostFnFromFunction; GCoptimization::EnergyType = long long int]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:235:30:   required from ‘void GCoptimization::specializeDataCostFunctor(UserFunctor) [with UserFunctor = GCoptimization::DataCostFnFromFunction]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:717:54:   required from here

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

   DataCostT& m_dc;
              ^

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

   SiteID m_site;
          ^

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

   GreedyIter(DataCostT& dc, SiteID numSites)
   ^
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.h: In instantiation of ‘GCoptimization::GreedyIter<DataCostT>::GreedyIter(DataCostT&, GCoptimization::SiteID) [with DataCostT = GCoptimization::DataCostFnFromFunctionExtra; GCoptimization::SiteID = int]’:
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:591:45:   required from ‘GCoptimization::EnergyType GCoptimization::solveGreedy() [with DataCostT = GCoptimization::DataCostFnFromFunctionExtra; GCoptimization::EnergyType = long long int]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:510:35:   required from ‘bool GCoptimization::solveSpecialCases(GCoptimization::EnergyType&) [with DataCostT = GCoptimization::DataCostFnFromFunctionExtra; GCoptimization::EnergyType = long long int]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:235:30:   required from ‘void GCoptimization::specializeDataCostFunctor(UserFunctor) [with UserFunctor = GCoptimization::DataCostFnFromFunctionExtra]’
/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:725:70:   required from here

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

   DataCostT& m_dc;
              ^

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

   SiteID m_site;
          ^

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

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

/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.cpp:1514:38: 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/cip/CIP/Utilities/GraphCutsOptimization -I/cip/CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include -I/cip/CIP-build/CIPPython-install/include/python2.7 -c /cip/CIP/Utilities/GraphCutsOptimization/graph.cpp -o build/temp.linux-x86_64-2.7/cip/CIP/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/cip/CIP/Utilities/GraphCutsOptimization -I/cip/CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include -I/cip/CIP-build/CIPPython-install/include/python2.7 -c /cip/CIP/Utilities/GraphCutsOptimization/LinkedBlockList.cpp -o build/temp.linux-x86_64-2.7/cip/CIP/Utilities/GraphCutsOptimization/LinkedBlockList.o

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

/cip/CIP/Utilities/GraphCutsOptimization/LinkedBlockList.cpp: In member function ‘void LinkedBlockList::addFront(ListType)’:

/cip/CIP/Utilities/GraphCutsOptimization/LinkedBlockList.cpp:18:35: warning: array subscript has type ‘char’ [-Wchar-subscripts]

  m_head ->m_item[m_head_block_size] = item;
                                   ^
/cip/CIP/Utilities/GraphCutsOptimization/LinkedBlockList.cpp: In member function ‘void* LinkedBlockList::next()’:

/cip/CIP/Utilities/GraphCutsOptimization/LinkedBlockList.cpp:26:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]

  ListType toReturn = m_cursor -> m_item[m_cursor_ind];
                                                     ^
/usr/bin/cc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/cip/CIP/Utilities/GraphCutsOptimization -I/cip/CIP-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include -I/cip/CIP-build/CIPPython-install/include/python2.7 -c /cip/CIP/Utilities/GraphCutsOptimization/maxflow.cpp -o build/temp.linux-x86_64-2.7/cip/CIP/Utilities/GraphCutsOptimization/maxflow.o

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

/usr/bin/c++ -pthread -shared -B /cip/CIP-build/CIPPython-install/compiler_compat -L/cip/CIP-build/CIPPython-install/lib -Wl,-rpath=/cip/CIP-build/CIPPython-install/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cip/CIP/cip_python/utils/gco_python/gco_python.o build/temp.linux-x86_64-2.7/cip/CIP/Utilities/GraphCutsOptimization/GCoptimization.o build/temp.linux-x86_64-2.7/cip/CIP/Utilities/GraphCutsOptimization/graph.o build/temp.linux-x86_64-2.7/cip/CIP/Utilities/GraphCutsOptimization/LinkedBlockList.o build/temp.linux-x86_64-2.7/cip/CIP/Utilities/GraphCutsOptimization/maxflow.o -L/cip/CIP/Utilities/GraphCutsOptimization -L/cip/CIP-build/CIPPython-install/lib -lpython2.7 -o /cip/CIP-build/CIP-build/cip_python/utils/pygco.so
[ 10%] Built target CIP_PYTHON
Scanning dependencies of target cipNelderMeadSimplexOptimizerTEST
[ 10%] Building CXX object Common/Testing/CMakeFiles/cipNelderMeadSimplexOptimizerTEST.dir/cipNelderMeadSimplexOptimizerTEST.cxx.o
[ 11%] Linking CXX executable cipNelderMeadSimplexOptimizerTEST
[ 11%] Built target cipNelderMeadSimplexOptimizerTEST
Scanning dependencies of target itkCIPExtractChestLabelMapImageFilterTEST
[ 11%] Building CXX object Common/Testing/CMakeFiles/itkCIPExtractChestLabelMapImageFilterTEST.dir/itkCIPExtractChestLabelMapImageFilterTEST.cxx.o
[ 11%] Linking CXX executable itkCIPExtractChestLabelMapImageFilterTEST
[ 11%] Built target itkCIPExtractChestLabelMapImageFilterTEST