new install fails ' Unsupported compiler '

[pcvdwh]

After removing all of R including packages and resources, it was time for a new R install. Upon reinstalling ANTsR it fails to install ANTsRCore with an 'unsupported compiler' issue.
ITKR installed without any issues.

Have tried several install routes with identical behaviour:

• devtools library( devtools ) install_github("stnava/ANTsR")
• command line git clone https://github.com/ANTsX/ANTsRCore.git R CMD INSTALL ANTsRCore
• binaries R CMD INSTALL ANTsRCore-0.7.0.0.0.tar.gz

System specs: R 3.6.1 macOS: 10.14.6-x86_64 CLT: 10.3.0.0.1.1562985497 Xcode: 10.3 CLT headers: 10.3.0.0.1.1562985497

Seems like CommandLineTools are installed and cmake is recent for both user and root:

xcode-select --version
xcode-select version 2354.

cmake -version
cmake version 3.15.2

This is the output. Any suggestions appreciated:

Downloading GitHub repo stnava/ANTsR@master Your system is ready to build packages! Downloading GitHub repo ANTsX/ANTsRCore@master Your system is ready to build packages! checking DESCRIPTION meta-information ...2/lqj1f0q542343139469pwxkr0000gp/T/RtmpiuSMES/remotesd4f44960065/ANTsX-ANTsRCore-e4090ac/DESCRIPTION’ ...

• installing source package ‘ANTsRCore’ ... ** using staged installation Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1 darwin18 1 fatal: not a git repository (or any of the parent directories): .git Cloning into 'ants'... Already on 'master' Your branch is up to date with 'origin/master'. Already up to date. Note: checking out '680942c1628c8ed142c6b25a4c8b9e47aadf3e01'.

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:

git checkout -b

HEAD is now at 680942c1 BUG: antsApplyTransforms -e 4 would write input image rather than deformed image -- The C compiler identification is AppleClang 10.0.1.10010046 -- The CXX compiler identification is AppleClang 10.0.1.10010046 -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test C_HAS_WARNING-Wno-uninitialized -- Performing Test C_HAS_WARNING-Wno-uninitialized - Success -- Performing Test C_HAS_WARNING-Wno-unused-parameter -- Performing Test C_HAS_WARNING-Wno-unused-parameter - Success -- Performing Test C_HAS_WARNING-Wall -- Performing Test C_HAS_WARNING-Wall - Success -- Performing Test C_HAS_WARNING-Wcast-align -- Performing Test C_HAS_WARNING-Wcast-align - Success -- Performing Test C_HAS_WARNING-Wdisabled-optimization -- Performing Test C_HAS_WARNING-Wdisabled-optimization - Success -- Performing Test C_HAS_WARNING-Wextra -- Performing Test C_HAS_WARNING-Wextra - Success -- Performing Test C_HAS_WARNING-Wformat=2 -- Performing Test C_HAS_WARNING-Wformat=2 - Success -- Performing Test C_HAS_WARNING-Winvalid-pch -- Performing Test C_HAS_WARNING-Winvalid-pch - Success -- Performing Test C_HAS_WARNING-Wno-format-nonliteral -- Performing Test C_HAS_WARNING-Wno-format-nonliteral - Success -- Performing Test C_HAS_WARNING-Wpointer-arith -- Performing Test C_HAS_WARNING-Wpointer-arith - Success -- Performing Test C_HAS_WARNING-Wshadow -- Performing Test C_HAS_WARNING-Wshadow - Success -- Performing Test C_HAS_WARNING-Wunused -- Performing Test C_HAS_WARNING-Wunused - Success -- Performing Test C_HAS_WARNING-Wwrite-strings -- Performing Test C_HAS_WARNING-Wwrite-strings - Success -- Performing Test C_HAS_WARNING-funit-at-a-time -- Performing Test C_HAS_WARNING-funit-at-a-time - Success -- Performing Test C_HAS_WARNING-Wno-strict-overflow -- Performing Test C_HAS_WARNING-Wno-strict-overflow - Success -- Performing Test CXX_HAS_WARNING-Wall -- Performing Test CXX_HAS_WARNING-Wall - Success -- Performing Test CXX_HAS_WARNING-Wcast-align -- Performing Test CXX_HAS_WARNING-Wcast-align - Success -- Performing Test CXX_HAS_WARNING-Wdisabled-optimization -- Performing Test CXX_HAS_WARNING-Wdisabled-optimization - Success -- Performing Test CXX_HAS_WARNING-Wextra -- Performing Test CXX_HAS_WARNING-Wextra - Success -- Performing Test CXX_HAS_WARNING-Wformat=2 -- Performing Test CXX_HAS_WARNING-Wformat=2 - Success -- Performing Test CXX_HAS_WARNING-Winvalid-pch -- Performing Test CXX_HAS_WARNING-Winvalid-pch - Success -- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral -- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral - Success -- Performing Test CXX_HAS_WARNING-Wpointer-arith -- Performing Test CXX_HAS_WARNING-Wpointer-arith - Success -- Performing Test CXX_HAS_WARNING-Wshadow -- Performing Test CXX_HAS_WARNING-Wshadow - Success -- Performing Test CXX_HAS_WARNING-Wunused -- Performing Test CXX_HAS_WARNING-Wunused - Success -- Performing Test CXX_HAS_WARNING-Wwrite-strings -- Performing Test CXX_HAS_WARNING-Wwrite-strings - Success -- Performing Test CXX_HAS_WARNING-funit-at-a-time -- Performing Test CXX_HAS_WARNING-funit-at-a-time - Success -- Performing Test CXX_HAS_WARNING-Wno-strict-overflow -- Performing Test CXX_HAS_WARNING-Wno-strict-overflow - Success -- Performing Test CXX_HAS_WARNING-Wno-deprecated -- Performing Test CXX_HAS_WARNING-Wno-deprecated - Success -- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof -- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof - Success -- Performing Test CXX_HAS_WARNING-Woverloaded-virtual -- Performing Test CXX_HAS_WARNING-Woverloaded-virtual - Success -- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel -- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel - Failed -- Found Git: /usr/bin/git (found version "2.20.1 (Apple Git-117)") -- SuperBuild - ANTS => Requires ITKv5, -- SuperBuild - ITKv5[OK] -- SuperBuild - ANTS[OK] -- Configuring done -- Generating done -- Build files have been written to: /private/var/folders/x2/lqj1f0q542343139469pwxkr0000gp/T/RtmpqtFcFv/R.INSTALL54db723e4bd2/ANTsRCore/src/antb ** libs /usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.0/ -I/private/var/folders/x2/lqj1f0q542343139469pwxkr0000gp/T/RtmpqtFcFv/R.INSTALL54db723e4bd2/ANTsRCore/src -I/private/var/folders/x2/lqj1f0q542343139469pwxkr0000gp/T/RtmpqtFcFv/R.INSTALL54db723e4bd2/ANTsRCore/src/ants/Examples/include/ -I/private/var/folders/x2/lqj1f0q542343139469pwxkr0000gp/T/RtmpqtFcFv/R.INSTALL54db723e4bd2/ANTsRCore/src/ants/Utilities -I/private/var/folders/x2/lqj1f0q542343139469pwxkr0000gp/T/RtmpqtFcFv/R.INSTALL54db723e4bd2/ANTsRCore/src/ants/Examples/ -I../inst/include/ -I/private/var/folders/x2/lqj1f0q542343139469pwxkr0000gp/T/RtmpqtFcFv/R.INSTALL54db723e4bd2/ANTsRCore/src/ants/Tensor/ -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Atropos.cpp -o Atropos.o In file included from Atropos.cpp:5: In file included from /private/var/folders/x2/lqj1f0q542343139469pwxkr0000gp/T/RtmpqtFcFv/R.INSTALL54db723e4bd2/ANTsRCore/src/ants/Examples/include/ants.h:4: In file included from /private/var/folders/x2/lqj1f0q542343139469pwxkr0000gp/T/RtmpqtFcFv/R.INSTALL54db723e4bd2/ANTsRCore/src/ants/Utilities/itkSurfaceCurvatureBase.h:22: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.0/itkObject.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.0/itkLightObject.h:21: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.0/itkMacro.h:42: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.0/itkConfigure.h:22: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.0/itk_compiler_detection.h:158:6: error: Unsupported compiler

error Unsupported compiler

 ^

1 error generated. make: *** [Atropos.o] Error 1 ERROR: compilation failed for package ‘ANTsRCore’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ANTsRCore’ Error: Failed to install 'ANTsR' from GitHub: Failed to install 'ANTsRCore' from GitHub: (converted from warning) installation of package ‘/var/folders/x2/lqj1f0q542343139469pwxkr0000gp/T//RtmpiuSMES/filed4f53f40a10/ANTsRCore_0.7.0.tar.gz’ had non-zero exit status

Thanks for your work and support! Philip

[muschellij2]

Please see https://github.com/ANTsX/ANTsR/issues/255.

Notably, did you install ITKR and ANTsRCore from source or a binary?

[pcvdwh]

I had looked at #255, but the cmake version does not seem to be the problem. Aha, see what you mean. I must have selected the source and not the binary. Stupid! Works like a charm now. Thanks a lot!