Build failures on Windows for conda-forge package

[ghisvail]

When did the error occur?

[ ] CMake configuration (cmake / ccmake)
[x] Compilation (make)
[ ] Installation (make install)

Build environment

• OS: Windows
• Type of system: conda-forge CI

ANTs version

Version 2.4.4

Build configuration and logs

https://dev.azure.com/conda-forge/84710dde-1620-425b-80d0-4cf5baca359d/_apis/build/builds/717445/logs/25

Additional context

I have resumed my effort for providing a Conda package for ANTs via conda-forge. It builds fine on Linux and macOS but fails on Windows with a linking error.

2023-06-03T20:49:24.5910710Z [20/427] Linking CXX executable Examples\antsAffineInitializer.exe
2023-06-03T20:49:24.5911565Z FAILED: Examples/antsAffineInitializer.exe 
2023-06-03T20:49:24.5913080Z cmd.exe /C "cd . && %BUILD_PREFIX%\Library\bin\cmake.exe -E vs_link_exe --intdir=Examples\CMakeFiles\antsAffineInitializer.dir --rc=C:\PROGRA~2\WI3CF2~1\10\bin\100226~1.0\x64\rc.exe --mt=C:\PROGRA~2\WI3CF2~1\10\bin\100226~1.0\x64\mt.exe --manifests  -- C:\PROGRA~2\MICROS~2\2019\ENTERP~1\VC\Tools\MSVC\1429~1.301\bin\Hostx64\x64\link.exe /nologo @CMakeFiles\antsAffineInitializer.rsp  /out:Examples\antsAffineInitializer.exe /implib:Examples\antsAffineInitializer.lib /pdb:Examples\antsAffineInitializer.pdb /version:0.0 /machine:x64  /INCREMENTAL:NO /subsystem:console  && cd ."
2023-06-03T20:49:24.5916778Z LINK: command "C:\PROGRA~2\MICROS~2\2019\ENTERP~1\VC\Tools\MSVC\1429~1.301\bin\Hostx64\x64\link.exe /nologo @CMakeFiles\antsAffineInitializer.rsp /out:Examples\antsAffineInitializer.exe /implib:Examples\antsAffineInitializer.lib /pdb:Examples\antsAffineInitializer.pdb /version:0.0 /machine:x64 /INCREMENTAL:NO /subsystem:console /MANIFEST /MANIFESTFILE:Examples\antsAffineInitializer.exe.manifest" failed (exit code 1169) with the following output:
2023-06-03T20:49:24.5919417Z LINK : warning LNK4044: unrecognized option '/lpthreads'; ignored
2023-06-03T20:49:24.5920686Z ITKOptimizers-5.3.lib(ITKOptimizers-5.3.dll) : error LNK2005: "protected: __cdecl itk::CostFunctionTemplate<double>::CostFunctionTemplate<double>(void)" (??0?$CostFunctionTemplate@N@itk@@IEAA@XZ) already defined in antsUtilities.lib(antsRegistration4DDouble.cxx.obj)
2023-06-03T20:49:24.5922719Z ITKOptimizers-5.3.lib(ITKOptimizers-5.3.dll) : error LNK2005: "protected: virtual __cdecl itk::CostFunctionTemplate<double>::~CostFunctionTemplate<double>(void)" (??1?$CostFunctionTemplate@N@itk@@MEAA@XZ) already defined in antsUtilities.lib(antsRegistration4DDouble.cxx.obj)
2023-06-03T20:49:24.5924701Z ITKOptimizers-5.3.lib(ITKOptimizers-5.3.dll) : error LNK2005: "protected: virtual void __cdecl itk::CostFunctionTemplate<double>::PrintSelf(class std::basic_ostream<char,struct std::char_traits<char> > &,class itk::Indent)const " (?PrintSelf@?$CostFunctionTemplate@N@itk@@MEBAXAEAV?$basic_ostream@DU?$char_traits@D@std@@@std@@VIndent@2@@Z) already defined in antsUtilities.lib(antsRegistration4DDouble.cxx.obj)
2023-06-03T20:49:38.3031489Z Examples\antsAffineInitializer.exe : fatal error LNK1169: one or more multiply defined symbols found

I would not mind skipping the Windows builds, but since you all made the efforts to provide Windows binaries lately, I was hopeful we could make it happen too for Conda.

[cookpa]

Thanks for working on this. The only Windows builds I do are via the Actions workflow, so unless anyone else can help, you might have to go ahead without Windows.

[cookpa]

I noticed while working on ANTsPy that the Windows builds there all turn shared libraries off (eg ANTsX/ANTsPy#345). I'm guessing that Conda needs shared libs turned on, but maybe this context will help narrow the search for solutions.

[cookpa]

Further update: Superbuild works on Windows with shared libs. So ANTs can build on Windows with shared libs on, so maybe the error is specific to using system ITK on Windows.

https://github.com/cookpa/ANTs/actions/runs/5291048324

Edit to add runner info:

CMake 3.26.4
Building for: Visual Studio 17 2022
-- The C compiler identification is MSVC 19.36.32532.0
-- The CXX compiler identification is MSVC 19.36.32532.0

[cookpa]

Thanks for all your efforts on this, @ghisvail !

[ghisvail]

ANTs is now available on conda-forge 🥳

I am trying my best to enable builds for Windows.

[ntustison]

Awesome. Thanks for this.

[ghisvail]

Still no luck with Windows on the conda-forge CI setup. No idea why I get these link errors for multiple definitions on Windows and not on macOS and Linux.

[20/426] Linking CXX executable Examples\antsAffineInitializer.exe
FAILED: Examples/antsAffineInitializer.exe 
cmd.exe /C "cd . && %BUILD_PREFIX%\Library\bin\cmake.exe -E vs_link_exe --intdir=Examples\CMakeFiles\antsAffineInitializer.dir --rc=C:\PROGRA~2\WI3CF2~1\10\bin\100226~1.0\x64\rc.exe --mt=C:\PROGRA~2\WI3CF2~1\10\bin\100226~1.0\x64\mt.exe --manifests  -- C:\PROGRA~1\MICROS~2\2022\ENTERP~1\VC\Tools\MSVC\1429~1.301\bin\HostX64\x64\link.exe /nologo @CMakeFiles\antsAffineInitializer.rsp  /out:Examples\antsAffineInitializer.exe /implib:Examples\antsAffineInitializer.lib /pdb:Examples\antsAffineInitializer.pdb /version:0.0 /machine:x64  /INCREMENTAL:NO /subsystem:console  && cd ."
LINK: command "C:\PROGRA~1\MICROS~2\2022\ENTERP~1\VC\Tools\MSVC\1429~1.301\bin\HostX64\x64\link.exe /nologo @CMakeFiles\antsAffineInitializer.rsp /out:Examples\antsAffineInitializer.exe /implib:Examples\antsAffineInitializer.lib /pdb:Examples\antsAffineInitializer.pdb /version:0.0 /machine:x64 /INCREMENTAL:NO /subsystem:console /MANIFEST /MANIFESTFILE:Examples\antsAffineInitializer.exe.manifest" failed (exit code 1169) with the following output:
LINK : warning LNK4044: unrecognized option '/lpthreads'; ignored
ITKOptimizers-5.3.lib(ITKOptimizers-5.3.dll) : error LNK2005: "protected: __cdecl itk::CostFunctionTemplate<double>::CostFunctionTemplate<double>(void)" (??0?$CostFunctionTemplate@N@itk@@IEAA@XZ) already defined in antsUtilities.lib(antsRegistration4DDouble.cxx.obj)
ITKOptimizers-5.3.lib(ITKOptimizers-5.3.dll) : error LNK2005: "protected: virtual __cdecl itk::CostFunctionTemplate<double>::~CostFunctionTemplate<double>(void)" (??1?$CostFunctionTemplate@N@itk@@MEAA@XZ) already defined in antsUtilities.lib(antsRegistration4DDouble.cxx.obj)
ITKOptimizers-5.3.lib(ITKOptimizers-5.3.dll) : error LNK2005: "protected: virtual void __cdecl itk::CostFunctionTemplate<double>::PrintSelf(class std::basic_ostream<char,struct std::char_traits<char> > &,class itk::Indent)const " (?PrintSelf@?$CostFunctionTemplate@N@itk@@MEBAXAEAV?$basic_ostream@DU?$char_traits@D@std@@@std@@VIndent@2@@Z) already defined in antsUtilities.lib(antsRegistration4DDouble.cxx.obj)
Examples\antsAffineInitializer.exe : fatal error LNK1169: one or more multiply defined symbols found

[cookpa]

It is a mystery. Are you sure that the ITK build you are linking against was compiled with the same settings? I read that incompatible compilers can cause this error.

[ghisvail]

Are you sure that the ITK build you are linking against was compiled with the same settings?

I just checked, both are compiled with the same compiler (vs2019) according to their CI manifests.

[cookpa]

I found an example of the same problem: https://discourse.itk.org/t/link-error-on-declaring-metrics-in-two-different-classes/2600

It seems like might be solvable on the ANTs side by resolving the duplicate imports, but would probably involve a lot of work. I guess other platform compilers are tolerant of these conflicts somehow.