Error with macOS-x86_64 and macOS-arm64

Hi all, I am running Geant4 using MATLAB (with a .sh script triggered by the "system" command)
In the .sh file I navigate to a build file and do "cmake -S .. -B ." 
After this I did "make -j 10" and got this is error message (any help would be greatly appreciated):

ld: warning: ld: warning: ignoring file /usr/local/Geant4/lib/libG4gl2ps.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ignoring file /usr/local/Geant4/lib/libG4GMocren.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4RayTracer.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4Tree.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4vis_management.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64ld: warning: ignoring file /usr/local/Geant4/lib/libG4FR.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64

ld: warning: ignoring file /usr/local/Geant4/lib/libG4OpenGL.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4modeling.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4VRML.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4visHepRep.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4readout.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4interfaces.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4parmodels.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4persistency.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtOpenGL.framework/QtOpenGL, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4physicslists.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4error_propagation.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4tasking.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtPrintSupport.framework/QtPrintSupport, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtCore.framework/QtCore, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtGui.framework/QtGui, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4run.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4event.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtWidgets.framework/QtWidgets, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4tools.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4analysis.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4processes.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4tracking.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4track.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4particles.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4digits_hits.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4zlib.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4geometry.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4graphics_reps.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4materials.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4intercoms.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4global.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4clhep.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4ptl.0.0.2.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
Undefined symbols for architecture x86_64:
“G4Exception(char const*, char const*, G4ExceptionSeverity, char const*)”, referenced from:
G4PSFlatSurfaceCircularCurrent::SetUnit(G4String const&) in G4PSFlatSurfaceCircularCurrent.cc.o
G4PSFlatSurfaceCircularFlux::SetUnit(G4String const&) in G4PSFlatSurfaceCircularFlux.cc.o
“aCountedObjectAllocator()”, referenced from:
G4PSFlatSurfaceCircularCurrent::ProcessHits(G4Step*, G4TouchableHistory*) in G4PSFlatSurfaceCircularCurrent.cc.o
G4PSFlatSurfaceCircularCurrent::IsSelectedSurface(G4Step*, G4Tubs*) in G4PSFlatSurfaceCircularCurrent.cc.o
G4PSFlatSurfaceCircularFlux::ProcessHits(G4Step*, G4TouchableHistory*) in G4PSFlatSurfaceCircularFlux.cc.o
G4PSFlatSurfaceCircularFlux::IsSelectedSurface(G4Step*, G4Tubs*) in G4PSFlatSurfaceCircularFlux.cc.o
“_G4cout_p()”, referenced from:
G4PSFlatSurfaceCircularCurrent::PrintAll() in G4PSFlatSurfaceCircularCurrent.cc.o
G4VTHitsMap<double, std::__1::map<int, double*, std::__1::less, std::__1::allocator<std::__1::pair<int const, double*> > > >::PrintAllHits() in G4PSFlatSurfaceCircularCurrent.cc.o
G4PSFlatSurfaceCircularFlux::PrintAll() in G4PSFlatSurfaceCircularFlux.cc.o
G4VTHitsMap<double, std::__1::map<int, double*, std::__1::less, std::__1::allocator<std::__1::pair<int const, double*> > > >::PrintAllHits() in G4PSFlatSurfaceCircularFlux.cc.o
RE02PSFlatSurfaceCurrent::GetIndex(G4Step*) in RE02PSFlatSurfaceCurrent.cc.o
RE02Run::RecordEvent(G4Event const*) in RE02Run.cc.o

“G4DAWNFILE::G4DAWNFILE()”, referenced from:
G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
“G4Material::AddMaterial(G4Material*, double)”, referenced from:
RE02DetectorConstruction::Construct() in RE02DetectorConstruction.cc.o
“G4Material::GetMaterial(G4String const&, bool)”, referenced from:
RE02DetectorConstruction::Construct() in RE02DetectorConstruction.cc.o
“G4Material::G4Material(G4String const&, double, int, G4State, double, double)”, referenced from:
RE02DetectorConstruction::Construct() in RE02DetectorConstruction.cc.o
“G4ASCIITree::G4ASCIITree()”, referenced from:
G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
“G4PSNofStep::EndOfEvent(G4HCofThisEvent*)”, referenced from:
vtable for RE02PSNofStep in RE02PSNofStep.cc.o
“G4PSNofStep::Initialize(G4HCofThisEvent*)”, referenced from:
vtable for RE02PSNofStep in RE02PSNofStep.cc.o
“G4PSNofStep::ProcessHits(G4Step*, G4TouchableHistory*)”, referenced from:
vtable for RE02PSNofStep in RE02PSNofStep.cc.o
“G4PSNofStep::clear()”, referenced from:
vtable for RE02PSNofStep in RE02PSNofStep.cc.o
“G4PSNofStep::DrawAll()”, referenced from:
vtable for RE02PSNofStep in RE02PSNofStep.cc.o
“G4PSNofStep::SetUnit(G4String const&)”, referenced from:
vtable for RE02PSNofStep in RE02PSNofStep.cc.o
“G4PSNofStep::PrintAll()”, referenced from:
vtable for RE02PSNofStep in RE02PSNofStep.cc.o
“G4PSNofStep::G4PSNofStep(G4String, int)”, referenced from:
RE02PSNofStep::RE02PSNofStep(G4String, int, int, int) in RE02PSNofStep.cc.o
RE02PSNofStep::RE02PSNofStep(G4String, int, int, int) in RE02PSNofStep.cc.o
“G4PSNofStep::~G4PSNofStep()”, referenced from:
RE02PSNofStep::~RE02PSNofStep() in RE02PSNofStep.cc.o
RE02PSNofStep::~RE02PSNofStep() in RE02PSNofStep.cc.o
RE02PSNofStep::~RE02PSNofStep() in RE02PSNofStep.cc.o
“G4RayTracer::G4RayTracer()”, referenced from:
G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
“G4SDManager::GetSDMpointer()”, referenced from:
RE02DetectorConstruction::ConstructSDandField() in RE02DetectorConstruction.cc.o
RE02Run::RE02Run(std::__1::vector<G4String, std::__1::allocator >) in RE02Run.cc.o
“G4SDManager::AddNewDetector(G4VSensitiveDetector*)”, referenced from:
RE02DetectorConstruction::ConstructSDandField() in RE02DetectorConstruction.cc.o
“G4SDManager::GetCollectionID(G4String)”, referenced from:
RE02Run::RE02Run(std::__1::vector<G4String, std::__1::allocator >) in RE02Run.cc.o
“G4SDManager::FindSensitiveDetector(G4String, bool)”, referenced from:
RE02Run::RE02Run(std::__1::vector<G4String, std::__1::allocator >) in RE02Run.cc.o
“G4Threading::G4GetNumberOfCores()”, referenced from:
_main in RE02.cc.o
“G4UImanager::ApplyCommand(G4String const&)”, referenced from:
_main in RE02.cc.o
“G4UImanager::GetUIpointer()”, referenced from:
_main in RE02.cc.o
“G4VRML2File::G4VRML2File()”, referenced from:
G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
“G4HepRepFile::G4HepRepFile()”, referenced from:
G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
“G4PSCellFlux::EndOfEvent(G4HCofThisEvent*)”, referenced from:
vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
“G4PSCellFlux::Initialize(G4HCofThisEvent*)”, referenced from:
vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
“G4PSCellFlux::ProcessHits(G4Step*, G4TouchableHistory*)”, referenced from:
vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
“G4PSCellFlux::ComputeVolume(G4Step*, int)”, referenced from:
vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
“G4PSCellFlux::DefineUnitAndCategory()”, referenced from:
vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
“G4PSCellFlux::clear()”, referenced from:
vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
“G4PSCellFlux::DrawAll()”, referenced from:
vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
“G4PSCellFlux::SetUnit(G4String const&)”, referenced from:
vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
“G4PSCellFlux::PrintAll()”, referenced from:
vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
“G4PSCellFlux::G4PSCellFlux(G4String, int)”, referenced from:
RE02PSCellFlux::RE02PSCellFlux(G4String, int, int, int) in RE02PSCellFlux.cc.o
RE02PSCellFlux::RE02PSCellFlux(G4String, int, int, int) in RE02PSCellFlux.cc.o
“G4PSCellFlux::~G4PSCellFlux()”, referenced from:
RE02PSCellFlux::~RE02PSCellFlux() in RE02PSCellFlux.cc.o
RE02PSCellFlux::~RE02PSCellFlux() in RE02PSCellFlux.cc.o
RE02PSCellFlux::~RE02PSCellFlux() in RE02PSCellFlux.cc.o
“G4RunManager::GetRunManager()”, referenced from:
RE02RunAction::EndOfRunAction(G4Run const*) in RE02RunAction.cc.o
“G4VisManager::FilterDigi(G4VDigi const&)”, referenced from:
vtable for G4VisExecutive in RE02.cc.o
(ELIMINATED SOME MORE OF THESE MESSAGES HERE)
NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
“virtual thunk to G4VModularPhysicsList::~G4VModularPhysicsList()”, referenced from:
construction vtable for G4VModularPhysicsList-in-MyPhysicsList in RE02Physics.cc.o
“virtual thunk to G4VModularPhysicsList::~G4VModularPhysicsList()”, referenced from:
construction vtable for G4VModularPhysicsList-in-MyPhysicsList in RE02Physics.cc.o
“virtual thunk to G4VModularPhysicsList::ConstructParticle()”, referenced from:
vtable for MyPhysicsList in RE02Physics.cc.o
construction vtable for G4VModularPhysicsList-in-MyPhysicsList in RE02Physics.cc.o
“virtual thunk to G4VModularPhysicsList::ConstructProcess()”, referenced from:
vtable for MyPhysicsList in RE02Physics.cc.o
construction vtable for G4VModularPhysicsList-in-MyPhysicsList in RE02Physics.cc.o
“virtual thunk to G4VModularPhysicsList::TerminateWorker()”, referenced from:
vtable for MyPhysicsList in RE02Physics.cc.o
construction vtable for G4VModularPhysicsList-in-MyPhysicsList in RE02Physics.cc.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [CMakeFiles/RE02.dir/build.make:458: RE02] Error 1
make[1]: *** [CMakeFiles/Makefile2:83: CMakeFiles/RE02.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
./Test_run.sh: line 24: ./RE02: No such file or directory

In a sense the error is obvious - the Geant4 being linked against was built for arm, but the built of the application is trying to do this for x86. Is this an x86 or arm Mac? Could you also post the output of the CMake run from a clean build, and also run make VERBOSE=1 and post one of the compilation commands in full so we can see what flags are being applied please?

Hi Benjamin, thanks for the message. This is an arm Mac. On my terminal in a “build_example” directory running

cmake -S .. -B .

yields:

(base) edwardt@onc-0986 build_example % cmake -S .. -B .
-- The C compiler identification is AppleClang 13.1.6.13160021
-- The CXX compiler identification is AppleClang 13.1.6.13160021
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found EXPAT: /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/lib/libexpat.tbd (found suitable version "2.4.1", minimum required is "2.4.1") 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Found OpenGL: /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/System/Library/Frameworks/OpenGL.framework   
-- Found Geant4: /usr/local/Geant4/lib/Geant4-11.0.2/Geant4Config.cmake (found version "11.0.2") 
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/edwardt/Documents/RE02_sensitivity_test/build_example

Then running:

make -j 10 VERBOSE=1

yields:

-- The C compiler identification is AppleClang 13.1.6.13160021
-- The CXX compiler identification is AppleClang 13.1.6.13160021
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found EXPAT: /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/lib/libexpat.tbd (found suitable version "2.4.1", minimum required is "2.4.1") 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Found OpenGL: /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/System/Library/Frameworks/OpenGL.framework   
-- Found Geant4: /usr/local/Geant4/lib/Geant4-11.0.2/Geant4Config.cmake (found version "11.0.2") 
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/edwardt/Documents/RE02_sensitivity_test/build_example
(base) edwardt@onc-0986 build_example % make -j 10 VERBOSE=1
/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -S/Users/edwardt/Documents/RE02_sensitivity_test -B/Users/edwardt/Documents/RE02_sensitivity_test/build_example --check-build-system CMakeFiles/Makefile.cmake 0
/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E cmake_progress_start /Users/edwardt/Documents/RE02_sensitivity_test/build_example/CMakeFiles /Users/edwardt/Documents/RE02_sensitivity_test/build_example//CMakeFiles/progress.marks
make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/Users/edwardt/Documents/RE02_sensitivity_test/build_example'
make  -f CMakeFiles/RE02.dir/build.make CMakeFiles/RE02.dir/depend
make[2]: Entering directory '/Users/edwardt/Documents/RE02_sensitivity_test/build_example'
cd /Users/edwardt/Documents/RE02_sensitivity_test/build_example && /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E cmake_depends "Unix Makefiles" /Users/edwardt/Documents/RE02_sensitivity_test /Users/edwardt/Documents/RE02_sensitivity_test /Users/edwardt/Documents/RE02_sensitivity_test/build_example/CMakeFiles/RE02.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/Users/edwardt/Documents/RE02_sensitivity_test/build_example'
make  -f CMakeFiles/RE02.dir/build.make CMakeFiles/RE02.dir/build
make[2]: Entering directory '/Users/edwardt/Documents/RE02_sensitivity_test/build_example'
[  4%] Building CXX object CMakeFiles/RE02.dir/src/Multitube_Parameterisation.cc.o
[  9%] Building CXX object CMakeFiles/RE02.dir/src/G4PSFlatSurfaceCircularFlux.cc.o
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/System/Library/Frameworks -iframework /opt/homebrew/opt/qt5/lib -isystem /opt/homebrew/opt/qt5/lib/QtGui.framework/Headers -isystem /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/System/Library/Frameworks/OpenGL.framework/Headers -isystem /opt/homebrew/opt/qt5/lib/QtCore.framework/Headers -isystem /opt/homebrew/opt/qt5/./mkspecs/macx-clang-arm64 -isystem /opt/homebrew/opt/qt5/lib/QtOpenGL.framework/Headers -isystem /opt/homebrew/opt/qt5/lib/QtWidgets.framework/Headers -isystem /opt/homebrew/opt/qt5/lib/QtPrintSupport.framework/Headers -W -Wall -pedantic -Wno-non-virtual-dtor -Wno-long-long -Wwrite-strings -Wpointer-arith -Woverloaded-virtual -Wno-variadic-macros -Wshadow -pipe -Qunused-arguments -DGL_SILENCE_DEPRECATION -pthread -ftls-model=initial-exec -std=c++17  -O3 -DNDEBUG -fno-trapping-math -ftree-vectorize -fno-math-errno -O3 -DNDEBUG -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk -fPIC -std=gnu++17 -MD -MT /Users/edwardt/Documents/RE02_sensitivity_test/src/Multitube_Parameterisation.cc
... other percentages
[ 36%] Building CXX object CMakeFiles/RE02.dir/src/RE02DetectorConstruction.cc.o
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/System/Library/Frameworks -iframework /opt/homebrew/opt/qt5/lib -isystem /opt/homebrew/opt/qt5/lib/QtGui.framework/Headers -isystem /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/System/Library/Frameworks/OpenGL.framework/Headers -isystem /opt/homebrew/opt/qt5/lib/QtCore.framework/Headers -isystem /opt/homebrew/opt/qt5/./mkspecs/macx-clang-arm64 -isystem /opt/homebrew/opt/qt5/lib/QtOpenGL.framework/Headers -isystem /opt/homebrew/opt/qt5/lib/QtWidgets.framework/Headers -isystem /opt/homebrew/opt/qt5/lib/QtPrintSupport.framework/Headers -W -Wall -pedantic -Wno-non-virtual-dtor -Wno-long-long -Wwrite-strings -Wpointer-arith -Woverloaded-virtual -Wno-variadic-macros -Wshadow -pipe -Qunused-arguments -DGL_SILENCE_DEPRECATION -pthread -ftls-model=initial-exec -std=c++17  -O3 -DNDEBUG -fno-trapping-math -ftree-vectorize -fno-math-errno -O3 -DNDEBUG -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk -fPIC -std=gnu++17 -MD -MT /Users/edwardt/Documents/RE02_sensitivity_test/src/RE02MFPSFlatSurfaceFlux.cc
[ 45%] Building CXX object CMakeFiles/RE02.dir/src/G4PSFlatSurfaceCircularCurrent.cc.o
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/System/Library/Frameworks -iframework /opt/homebrew/opt/qt5/lib -isystem /opt/homebrew/opt/qt5/lib/QtGui.framework/Headers -isystem /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/System/Library/Frameworks/OpenGL.framework/Headers -isystem /opt/homebrew/opt/qt5/lib/QtCore.framework/Headers -isystem /opt/homebrew/opt/qt5/./mkspecs/macx-clang-arm64 -isystem /opt/homebrew/opt/qt5/lib/QtOpenGL.framework/Headers -isystem /opt/homebrew/opt/qt5/lib/QtWidgets.framework/Headers -isystem /opt/homebrew/opt/qt5/lib/QtPrintSupport.framework/Headers -W -Wall -pedantic -Wno-non-virtual-dtor -Wno-long-long -Wwrite-strings -Wpointer-arith -Woverloaded-virtual -Wno-variadic-macros -Wshadow -pipe -Qunused-arguments -DGL_SILENCE_DEPRECATION -pthread -ftls-model=initial-exec -std=c++17  -O3 -DNDEBUG -fno-trapping-math -ftree-vectorize -fno-math-errno -O3 -DNDEBUG -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk -fPIC -std=gnu++17 -MD -MT CMakeFiles/RE02.dir/src/RE02EventAction.cc.o -MF CMakeFiles/RE02.dir/src/RE02EventAction.cc.o.d -o CMakeFiles/RE02.dir/src/RE02EventAction.cc.o -c /Users/edwardt/Documents/RE02_sensitivity_test/src/RE02EventAction.cc
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make[2]: Leaving directory '/Users/edwardt/Documents/RE02_sensitivity_test/build_example'
[100%] Built target RE02
make[1]: Leaving directory '/Users/edwardt/Documents/RE02_sensitivity_test/build_example'
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I got rid of some warnings and parameter shadowing. Also bare in mind this is taken from the terminal output. When I am trying to run from MATLAB system commands it does things differently. I will put this in another reply

I had to chop lots of bits out that were repeated so don’t be surprised if some obvious messages don’t pop out - they’ll be repeated somewhere at least once

from the MATLAB command line:
(in Test_run.sh it reads:

cmake -DCMAKE_INSTALL_PREFIX=/Users/edwardt/Documents/geant4-v11.0.2 -DCMAKE_PREFIX_PATH=$(brew --prefix qt@5) -S .. -B .
make -j 10 VERBOSE=1
>> system('./Test_run.sh')
/Users/edwardt/.zshrc: line 41: source: /opt/homebrew/opt/qt@5: is a directory
/Users/edwardt/.zshrc: line 43: source: /Users/edwardt/Documents/geant4-v11.0.2-build: is a directory
./Test_run.sh: line 22: brew: command not found
-- The C compiler identification is AppleClang 13.1.6.13160021
-- The CXX compiler identification is AppleClang 13.1.6.13160021
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found EXPAT: /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/lib/libexpat.tbd (found suitable version "2.4.1", minimum required is "2.4.1") 
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Found OpenGL: /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/System/Library/Frameworks/OpenGL.framework   
-- Found Geant4: /usr/local/Geant4/lib/Geant4-11.0.2/Geant4Config.cmake (found version "11.0.2") 
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/edwardt/Documents/RE02_sensitivity_test/build_2
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ld: warning: ignoring file /usr/local/Geant4/lib/libG4FR.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4GMocren.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4visHepRep.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4VRML.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
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ld: warning: ignoring file /usr/local/Geant4/lib/libG4RayTracer.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4OpenGL.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4vis_management.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4modeling.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4readout.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4interfaces.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4parmodels.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4persistency.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4physicslists.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4tasking.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4error_propagation.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4run.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtOpenGL.framework/QtOpenGL, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4tracking.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtCore.framework/QtCore, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtWidgets.framework/QtWidgets, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtGui.framework/QtGui, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4event.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/opt/qt5/lib/QtPrintSupport.framework/QtPrintSupport, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4processes.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4analysis.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4digits_hits.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4track.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4tools.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4particles.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4materials.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4graphics_reps.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4geometry.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4intercoms.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4global.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4zlib.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4clhep.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /usr/local/Geant4/lib/libG4ptl.0.0.2.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
Undefined symbols for architecture x86_64:
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      G4Tubs::SetZHalfLength(double) in Multitube_Parameterisation.cc.o
  "G4Exception(char const*, char const*, G4ExceptionSeverity, char const*)", referenced from:
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      G4PSFlatSurfaceCircularFlux::SetUnit(G4String const&) in G4PSFlatSurfaceCircularFlux.cc.o
  "aCountedObjectAllocator()", referenced from:
      G4PSFlatSurfaceCircularCurrent::ProcessHits(G4Step*, G4TouchableHistory*) in G4PSFlatSurfaceCircularCurrent.cc.o
      G4PSFlatSurfaceCircularCurrent::IsSelectedSurface(G4Step*, G4Tubs*) in G4PSFlatSurfaceCircularCurrent.cc.o
      G4PSFlatSurfaceCircularFlux::ProcessHits(G4Step*, G4TouchableHistory*) in G4PSFlatSurfaceCircularFlux.cc.o
      G4PSFlatSurfaceCircularFlux::IsSelectedSurface(G4Step*, G4Tubs*) in G4PSFlatSurfaceCircularFlux.cc.o
  "_G4cout_p()", referenced from:
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      G4VTHitsMap<double, std::__1::map<int, double*, std::__1::less<int>, std::__1::allocator<std::__1::pair<int const, double*> > > >::PrintAllHits() in G4PSFlatSurfaceCircularCurrent.cc.o
      G4PSFlatSurfaceCircularFlux::PrintAll() in G4PSFlatSurfaceCircularFlux.cc.o
      G4VTHitsMap<double, std::__1::map<int, double*, std::__1::less<int>, std::__1::allocator<std::__1::pair<int const, double*> > > >::PrintAllHits() in G4PSFlatSurfaceCircularFlux.cc.o
      Multifoil_Parameterisation::PrintParams() in Multifoil_Parameterisation.cc.o
      RE02PSFlatSurfaceCurrent::GetIndex(G4Step*) in RE02PSFlatSurfaceCurrent.cc.o
      RE02Run::RecordEvent(G4Event const*) in RE02Run.cc.o
      ...
  "G4DAWNFILE::G4DAWNFILE()", referenced from:
      G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
  "G4Material::AddMaterial(G4Material*, double)", referenced from:
      RE02DetectorConstruction::Construct() in RE02DetectorConstruction.cc.o
  "G4Material::GetMaterial(G4String const&, bool)", referenced from:
      RE02DetectorConstruction::Construct() in RE02DetectorConstruction.cc.o
  "G4Material::G4Material(G4String const&, double, int, G4State, double, double)", referenced from:
      RE02DetectorConstruction::Construct() in RE02DetectorConstruction.cc.o
  "G4ASCIITree::G4ASCIITree()", referenced from:
      G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
  "G4PSNofStep::EndOfEvent(G4HCofThisEvent*)", referenced from:
      vtable for RE02PSNofStep in RE02PSNofStep.cc.o
  "G4PSNofStep::Initialize(G4HCofThisEvent*)", referenced from:
      vtable for RE02PSNofStep in RE02PSNofStep.cc.o
  "G4PSNofStep::ProcessHits(G4Step*, G4TouchableHistory*)", referenced from:
      vtable for RE02PSNofStep in RE02PSNofStep.cc.o
  "G4PSNofStep::clear()", referenced from:
      vtable for RE02PSNofStep in RE02PSNofStep.cc.o
  "G4PSNofStep::DrawAll()", referenced from:
      vtable for RE02PSNofStep in RE02PSNofStep.cc.o
  "G4PSNofStep::SetUnit(G4String const&)", referenced from:
      vtable for RE02PSNofStep in RE02PSNofStep.cc.o
  "G4PSNofStep::PrintAll()", referenced from:
      vtable for RE02PSNofStep in RE02PSNofStep.cc.o
  "G4PSNofStep::G4PSNofStep(G4String, int)", referenced from:
      RE02PSNofStep::RE02PSNofStep(G4String, int, int, int) in RE02PSNofStep.cc.o
      RE02PSNofStep::RE02PSNofStep(G4String, int, int, int) in RE02PSNofStep.cc.o
  "G4PSNofStep::~G4PSNofStep()", referenced from:
      RE02PSNofStep::~RE02PSNofStep() in RE02PSNofStep.cc.o
      RE02PSNofStep::~RE02PSNofStep() in RE02PSNofStep.cc.o
      RE02PSNofStep::~RE02PSNofStep() in RE02PSNofStep.cc.o
  "G4RayTracer::G4RayTracer()", referenced from:
      G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
  "G4SDManager::GetSDMpointer()", referenced from:
      RE02DetectorConstruction::ConstructSDandField() in RE02DetectorConstruction.cc.o
      RE02Run::RE02Run(std::__1::vector<G4String, std::__1::allocator<G4String> >) in RE02Run.cc.o
  "G4SDManager::AddNewDetector(G4VSensitiveDetector*)", referenced from:
      RE02DetectorConstruction::ConstructSDandField() in RE02DetectorConstruction.cc.o
  "G4SDManager::GetCollectionID(G4String)", referenced from:
      RE02Run::RE02Run(std::__1::vector<G4String, std::__1::allocator<G4String> >) in RE02Run.cc.o
  "G4SDManager::FindSensitiveDetector(G4String, bool)", referenced from:
      RE02Run::RE02Run(std::__1::vector<G4String, std::__1::allocator<G4String> >) in RE02Run.cc.o
  "G4Threading::G4GetNumberOfCores()", referenced from:
      _main in RE02.cc.o
  "G4UImanager::ApplyCommand(G4String const&)", referenced from:
      _main in RE02.cc.o
  "G4UImanager::GetUIpointer()", referenced from:
      _main in RE02.cc.o
  "G4VRML2File::G4VRML2File()", referenced from:
      G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
  "G4HepRepFile::G4HepRepFile()", referenced from:
      G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
  "G4PSCellFlux::EndOfEvent(G4HCofThisEvent*)", referenced from:
      vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
  "G4PSCellFlux::Initialize(G4HCofThisEvent*)", referenced from:
      vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
  "G4PSCellFlux::ProcessHits(G4Step*, G4TouchableHistory*)", referenced from:
      vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
  "G4PSCellFlux::ComputeVolume(G4Step*, int)", referenced from:
      vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
  "G4PSCellFlux::DefineUnitAndCategory()", referenced from:
      vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
  "G4PSCellFlux::clear()", referenced from:
      vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
  "G4PSCellFlux::DrawAll()", referenced from:
      vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
  "G4PSCellFlux::SetUnit(G4String const&)", referenced from:
      vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
  "G4PSCellFlux::PrintAll()", referenced from:
      vtable for RE02PSCellFlux in RE02PSCellFlux.cc.o
  "G4PSCellFlux::G4PSCellFlux(G4String, int)", referenced from:
      RE02PSCellFlux::RE02PSCellFlux(G4String, int, int, int) in RE02PSCellFlux.cc.o
      RE02PSCellFlux::RE02PSCellFlux(G4String, int, int, int) in RE02PSCellFlux.cc.o
  "G4PSCellFlux::~G4PSCellFlux()", referenced from:
      RE02PSCellFlux::~RE02PSCellFlux() in RE02PSCellFlux.cc.o
      RE02PSCellFlux::~RE02PSCellFlux() in RE02PSCellFlux.cc.o
      RE02PSCellFlux::~RE02PSCellFlux() in RE02PSCellFlux.cc.o
  "G4RunManager::GetRunManager()", referenced from:
      RE02RunAction::EndOfRunAction(G4Run const*) in RE02RunAction.cc.o
  "G4VisManager::FilterDigi(G4VDigi const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Initialise()", referenced from:
      _main in RE02.cc.o
  "G4VisManager::BeginDraw2D(HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::NotifyHandlers()", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::DispatchToModel(G4VTrajectory const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::SetUpForAThread()", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::FilterTrajectory(G4VTrajectory const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::GeometryHasChanged()", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::IgnoreStateChanges(bool)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::RegisterModelFactory(G4VModelFactory<G4VTrajectoryModel>*)", referenced from:
      G4VisExecutive::RegisterModelFactories() in RE02.cc.o
  "G4VisManager::RegisterModelFactory(G4VModelFactory<G4VFilter<G4VTrajectory> >*)", referenced from:
      G4VisExecutive::RegisterModelFactories() in RE02.cc.o
  "G4VisManager::RegisterModelFactory(G4VModelFactory<G4VFilter<G4VHit> >*)", referenced from:
      G4VisExecutive::RegisterModelFactories() in RE02.cc.o
  "G4VisManager::RegisterModelFactory(G4VModelFactory<G4VFilter<G4VDigi> >*)", referenced from:
      G4VisExecutive::RegisterModelFactories() in RE02.cc.o
  "G4VisManager::RegisterGraphicsSystem(G4VGraphicsSystem*)", referenced from:
      G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
  "G4VisManager::Draw(G4Polyline const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4Polyhedron const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4Polymarker const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4VTrajectory const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4LogicalVolume const&, G4VisAttributes const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4VPhysicalVolume const&, G4VisAttributes const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4Text const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4VHit const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4VDigi const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4Circle const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4Square const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw(G4VSolid const&, G4VisAttributes const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw2D(G4Polyline const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw2D(G4Polyhedron const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw2D(G4Polymarker const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw2D(G4Text const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw2D(G4Circle const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::Draw2D(G4Square const&, HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::EndDraw()", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::BeginDraw(HepGeom::Transform3D const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::EndDraw2D()", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::FilterHit(G4VHit const&)", referenced from:
      vtable for G4VisExecutive in RE02.cc.o
  "G4VisManager::G4VisManager(G4String const&)", referenced from:
      _main in RE02.cc.o
  "G4VisManager::~G4VisManager()", referenced from:
      G4VisExecutive::~G4VisExecutive() in RE02.cc.o
      G4VisExecutive::~G4VisExecutive() in RE02.cc.o
  "G4GMocrenFile::G4GMocrenFile()", referenced from:
      G4VisExecutive::RegisterGraphicsSystems() in RE02.cc.o
  "G4NistManager::Instance()", referenced from:
      RE02DetectorConstruction::Construct() in RE02DetectorConstruction.cc.o
  "G4PVPlacement::G4PVPlacement(CLHEP::HepRotation*, CLHEP::Hep3Vector const&, G4LogicalVolume*, G4String const&, G4LogicalVolume*, bool, int, bool)", referenced from:
      RE02DetectorConstruction::Construct() in RE02DetectorConstruction.cc.o
  "G4ParticleGun::SetParticleEnergy(double)", referenced from:
      RE02PrimaryGeneratorAction::RE02PrimaryGeneratorAction() in RE02PrimaryGeneratorAction.cc.o
      RE02PrimaryGeneratorAction::GeneratePrimaries(G4Event*) in RE02PrimaryGeneratorAction.cc.o
  "G4ParticleGun::SetParticleDefinition(G4ParticleDefinition*)", referenced from:
      RE02PrimaryGeneratorAction::RE02PrimaryGeneratorAction() in RE02PrimaryGeneratorAction.cc.o
  "G4ParticleGun::G4ParticleGun(int)", referenced from:
      RE02PrimaryGeneratorAction::RE02PrimaryGeneratorAction() in RE02PrimaryGeneratorAction.cc.o
  "G4UIExecutive::G4UIExecutive(int, char**, G4String const&)", referenced from:
      _main in RE02.cc.o

Thanks for the detailed output! All I can spot is that there’s something going on in your .zshrc file and the Test_run.sh script:

There also appear to be differences in the CMake being run on the command line:

vs from the script:

So I would try running the script outside of Matlab first and get to the bottom of the error messages from .zshrc. I’d guess it’s the CMake being picked up from /Applications that’s the issue, but might point to something else.

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