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BICCN / cell-locator

manually align specimens to annotated 3D spaces
https://cell-locator.readthedocs.io
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Bundled ITK does not support GCC 9 #127

Closed allemangD closed 4 years ago

allemangD commented 4 years ago

Environment

Description Bundled ITK/VNL build fails with "dunno about this gcc" error. The issue is the same as described in this upstream ITK issue. It looks like there has been a patch for it, but the change is not present in any ITK 4 release.

Scanning dependencies of target ITKKWSys-all
[  1%] Built target ITKKWSys-all
[  1%] Building CXX object Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/vcl_deprecated.cxx.o
In file included from /.../ITK/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_iostream.h:5,
                 from /.../ITK/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_deprecated.cxx:4:
/.../ITK/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h:101:4: error: #error "Dunno about this gcc"
  101 | #  error "Dunno about this gcc"
      |    ^~~~~
make[6]: *** [Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/build.make:66: Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/vcl_deprecated.cxx.o] Error 1
make[5]: *** [CMakeFiles/Makefile2:5881: Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/all] Error 2
make[4]: *** [Makefile:155: all] Error 2
make[3]: *** [slicersources-build/CMakeFiles/ITK.dir/build.make:118: slicersources-build/ITK-prefix/src/ITK-stamp/ITK-build] Error 2
make[2]: *** [CMakeFiles/Makefile2:568: slicersources-build/CMakeFiles/ITK.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:575: slicersources-build/CMakeFiles/ITK.dir/rule] Error 2
make: *** [Makefile:316: ITK] Error 2

How to Reproduce

git clone git@github.com:BICCN/cell-locator.git
mkdir cell-locator-build
cd cell-locator-build
cmake -G 'Unix Makefiles' ../cell-locator
make ITK

Workaround Using gcc/g++ 8 via update-alternatives is sufficient to build ITK.