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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
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ANTsR compilation errors ("no member named ...") #291

Closed ntustison closed 4 years ago

ntustison commented 4 years ago

Hi all,

Just wondering if anybody has encountered a recent installation problem I'm struggling with. I recently upgraded to macOS 10.15.2 (Xcodebuild version 11.3). I can compile ANTs just fine. I've also completely removed the ITKR, ANTsRCore, and ANTsR libraries from the Resources/library subdirectory. Then, when I do

> devtools::install_github( "ANTsX/ANTsR" )

ITKR compiles just fine. However, the installation process halts immediately when trying to compile Atropos, i.e., see below. Has anybody seen this?

* installing *source* package ‘ANTsRCore’ ...
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
darwin19 1
fatal: not a git repository (or any of the parent directories): .git
Cloning into 'ants'...
remote: Enumerating objects: 24001, done.
remote: Total 24001 (delta 0), reused 0 (delta 0), pack-reused 24001
Receiving objects: 100% (24001/24001), 20.18 MiB | 4.55 MiB/s, done.
Resolving deltas: 100% (17066/17066), done.
Already on 'master'
Your branch is up to date with 'origin/master'.
Already up to date.
Note: checking out '416b9d10458f6bbf78e788b823ad0be9db11d7e8'.

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 <new-branch-name>

HEAD is now at 416b9d10 Merge pull request #904 from ANTsX/gcc-9-enhanced_warnings-round8
-- The C compiler identification is AppleClang 11.0.0.11000033
-- The CXX compiler identification is AppleClang 11.0.0.11000033
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/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: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Not using CCache
-- 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-Wno-long-double
-- Performing Test C_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-long-double
-- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-undefined-var-template
-- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - 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
-- Performing Test C_HAS_WARNING-mtune_native
-- Performing Test C_HAS_WARNING-mtune_native - Success
-- Performing Test C_HAS_WARNING-march_corei7
-- Performing Test C_HAS_WARNING-march_corei7 - Success
-- Performing Test CXX_HAS_WARNING-mtune_native
-- Performing Test CXX_HAS_WARNING-mtune_native - Success
-- Performing Test CXX_HAS_WARNING-march_corei7
-- Performing Test CXX_HAS_WARNING-march_corei7 - Success
-- Found Git: /usr/bin/git (found version "2.21.0 (Apple Git-122.2)") 
-- SuperBuild - ANTS => Requires ITKv5, 
-- SuperBuild -   ITKv5[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    COPY_SCRIPT_FILES_TO_BIN_DIR

-- Build files have been written to: /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/antb
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/ -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Examples/include/   -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Utilities -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Examples/ -I../inst/include/   -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Tensor/  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Atropos.cpp -o Atropos.o
In file included from Atropos.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:318:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:319:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:320:9: error: no member named 'isfinite' in the global namespace; did you
      mean 'finite'?
using ::isfinite;
      ~~^
/usr/local/include/math.h:749:12: note: 'finite' declared here
extern int finite(double)
           ^
In file included from Atropos.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:321:9: error: no member named 'isinf' in the global namespace
using ::isinf;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:322:9: error: no member named 'isnan' in the global namespace
using ::isnan;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:323:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:324:7: error: no member named 'isgreater' in the global namespace; did you
      mean '::std::greater'?
using ::isgreater;
      ^~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/functional:728:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                            ^
In file included from Atropos.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:325:7: error: no member named 'isgreaterequal' in the global namespace; did
      you mean '::std::greater_equal'?
using ::isgreaterequal;
      ^~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/functional:757:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                            ^
In file included from Atropos.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:326:9: error: no member named 'isless' in the global namespace
using ::isless;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:327:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:328:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:329:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:330:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
In file included from Atropos.cpp:5:
In file included from /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Examples/include/ants.h:4:
In file included from /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Utilities/itkSurfaceCurvatureBase.h:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkProcessObject.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkDomainThreader.h:22:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMultiThreaderBase.h:35:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkImageRegion.h:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkContinuousIndex.h:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkPoint.h:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.h:332:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.hxx:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:33:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/vnl/vnl_math.h:199:15: error: expected unqualified-id
  inline bool isinf(TArg arg) { return bool(std::isinf(arg)); }
              ^
/usr/local/include/math.h:160:7: note: expanded from macro 'isinf'
    ( sizeof(x) == sizeof(float)  ? __inline_isinff((float)(x))          \
      ^
In file included from Atropos.cpp:5:
In file included from /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Examples/include/ants.h:4:
In file included from /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Utilities/itkSurfaceCurvatureBase.h:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkProcessObject.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkDomainThreader.h:22:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMultiThreaderBase.h:35:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkImageRegion.h:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkContinuousIndex.h:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkPoint.h:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.h:332:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.hxx:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:33:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/vnl/vnl_math.h:199:15: error: expected ')'
/usr/local/include/math.h:160:7: note: expanded from macro 'isinf'
    ( sizeof(x) == sizeof(float)  ? __inline_isinff((float)(x))          \
      ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/vnl/vnl_math.h:199:15: note: to match this '('
/usr/local/include/math.h:160:5: note: expanded from macro 'isinf'
    ( sizeof(x) == sizeof(float)  ? __inline_isinff((float)(x))          \
    ^
In file included from Atropos.cpp:5:
In file included from /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Examples/include/ants.h:4:
In file included from /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Utilities/itkSurfaceCurvatureBase.h:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkProcessObject.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkDomainThreader.h:22:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMultiThreaderBase.h:35:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkImageRegion.h:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkContinuousIndex.h:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkPoint.h:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.h:332:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.hxx:21:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:770:12: error: no member named 'isnan' in namespace 'std'
using std::isnan;
      ~~~~~^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:771:12: error: no member named 'isinf' in namespace 'std'
using std::isinf;
      ~~~~~^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:772:12: error: no member named 'isfinite' in namespace 'std'; did you mean 'finite'?
using std::isfinite;
      ~~~~~^~~~~~~~
           finite
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:320:9: note: 'finite' declared here
using ::isfinite;
        ^
In file included from Atropos.cpp:5:
In file included from /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Examples/include/ants.h:4:
In file included from /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd3bd7b459/ANTsX-ANTsRCore-416d8f1/src/ants/Utilities/itkSurfaceCurvatureBase.h:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkProcessObject.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkDomainThreader.h:22:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMultiThreaderBase.h:35:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkImageRegion.h:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkContinuousIndex.h:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkPoint.h:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.h:332:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.hxx:21:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:773:12: error: no member named 'isnormal' in namespace 'std'
using std::isnormal;
      ~~~~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [Atropos.o] Error 1
ERROR: compilation failed for package ‘ANTsRCore’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ANTsRCore’
Installation failed: Command failed (1)
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/RtmplLn07r/devtoolsa7dd597540cf/ANTsX-ANTsR-f0187f8'  \
  --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library'  \
  --install-tests 

ERROR: dependency ‘ANTsRCore’ is not available for package ‘ANTsR’
stnava commented 4 years ago

Does

R CMD INSTALL

approach work?

ntustison commented 4 years ago

The same thing happens. I even messed with the clang++ command call because it looks to me, possibly being naive, that the wrong std library is being used.

muschellij2 commented 4 years ago

What's in /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1? Mine has no c++ folder Best, John

On Wed, Dec 11, 2019 at 5:51 PM Nick Tustison notifications@github.com wrote:

The same thing happens. I even messed with the clang++ command call because it looks to me, possibly being naive, that the wrong std library is being used.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/291?email_source=notifications&email_token=AAIGPLUC66VAA6NN3FGGXKTQYFVGLA5CNFSM4JZWDLU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGU3COQ#issuecomment-564769082, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIGPLWBP7HPVUKME76MNLTQYFVGLANCNFSM4JZWDLUQ .

ntustison commented 4 years ago

Thanks @muschellij2 Interesting. Mine doesn't either. I have

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/

but no c++ subfolder.

However, the complaints appear to be generated from subfolders in 

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/

which does have a c++ subfolder.

muschellij2 commented 4 years ago

Wonder if it's an Xcode mess up, as I see for clang: Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1

Best, John

On Wed, Dec 11, 2019 at 6:03 PM Nick Tustison notifications@github.com wrote:

Thanks @muschellij2 https://github.com/muschellij2 Interesting. Mine doesn't either. I have

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/

but no c++ subfolder.

However, the complaints appear to be generated from subfolders in

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/

which does have a c++ subfolder.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/291?email_source=notifications&email_token=AAIGPLSNSI4XIOMKF74UMMLQYFWUNA5CNFSM4JZWDLU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGU36CQ#issuecomment-564772618, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIGPLUVCQ2D6WHL237BFS3QYFWUNANCNFSM4JZWDLUQ .

muschellij2 commented 4 years ago

Ahh - likely not, I get:

gcc --version Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple clang version 11.0.0 (clang-1100.0.33.12) Target: x86_64-apple-darwin18.7.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Best, John

On Wed, Dec 11, 2019 at 6:04 PM John Muschelli muschellij2@gmail.com wrote:

Wonder if it's an Xcode mess up, as I see for clang: Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1

Best, John

On Wed, Dec 11, 2019 at 6:03 PM Nick Tustison notifications@github.com wrote:

Thanks @muschellij2 https://github.com/muschellij2 Interesting. Mine doesn't either. I have

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/

but no c++ subfolder.

However, the complaints appear to be generated from subfolders in

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/

which does have a c++ subfolder.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/291?email_source=notifications&email_token=AAIGPLSNSI4XIOMKF74UMMLQYFWUNA5CNFSM4JZWDLU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGU36CQ#issuecomment-564772618, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIGPLUVCQ2D6WHL237BFS3QYFWUNANCNFSM4JZWDLUQ .

ntustison commented 4 years ago

Yeah, I think you're right. And this certainly helps. Let me see if I can reconcile what is invoked on my machine with what you have.

muschellij2 commented 4 years ago

Just tried to install, mine has

-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

and your command does not. Likely a cause - gotta see your config. Maybe add: cat ~/.R/Makevars

See https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Recommended-C_002fC_002b_002b-compilers

Sedition here:

For macOS 10.14 (‘Mojave’) and versions 10.x of the Command Line Tools, an additional step is needed to install the headers to /usr/include: from a Terminal run

sudo installer -pkg \ /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \ -target / (This will need to be re-run if the OS decides to update the Command Line Tools.)

Alternatively, change the system paths via

CC="/usr/local/clang8/bin/clang -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" CXX="/usr/local/clang8/bin/clang++ -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" (The location of the SDK can be found by running xcrun -show-sdk-path.)

This alternative approach is needed for versions 11.x of the Command Line Tools/Xcode.

Best, John

On Wed, Dec 11, 2019 at 6:06 PM Nick Tustison notifications@github.com wrote:

Yeah, I think you're right. And this certainly helps. Let me see if I can reconcile what is invoked on my machine with what you have.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/291?email_source=notifications&email_token=AAIGPLRH2L2WKNZMXS2XQ2TQYFW67A5CNFSM4JZWDLU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGU4FDY#issuecomment-564773519, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIGPLX5KS66ICTCDHXBFCLQYFW67ANCNFSM4JZWDLUQ .

ntustison commented 4 years ago

Okay, took a little while to set up everything. So this is what is currently in make ~/.R/Makevars file:

CC=/usr/local/clang8/bin/clang -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXX=/usr/local/clang8/bin/clang++ -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXX11=/usr/local/clang8/bin/clang++ -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXX14=/usr/local/clang8/bin/clang++ -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXX17=/usr/local/clang8/bin/clang++ -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CFLAGS=-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXXFLAGS=-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXX11FLAGS=-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXX14FLAGS=-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXX17FLAGS=-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
FC=/usr/local/gfortran/bin/gfortran
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0  -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
LDFLAGS=-L/usr/local/clang8/lib -L/usr/local/lib
R_LD_LIBRARY_PATH=/usr/local/clang8/lib:/usr/local/lib

And I've made progress such that it looks like the specified clang++ is being used but I'm still ending up with similar errors:

-- Build files have been written to: /private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/Rtmpe8xnBk/devtools73e63aecbc58/ANTsX-ANTsRCore-416d8f1/src/antb
** libs
/usr/local/clang8/bin/clang++ -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/libs/include/ITK-5.1/ -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/Rtmpe8xnBk/devtools73e63aecbc58/ANTsX-ANTsRCore-416d8f1/src -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/Rtmpe8xnBk/devtools73e63aecbc58/ANTsX-ANTsRCore-416d8f1/src/ants/Examples/include/   -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/Rtmpe8xnBk/devtools73e63aecbc58/ANTsX-ANTsRCore-416d8f1/src/ants/Utilities -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/Rtmpe8xnBk/devtools73e63aecbc58/ANTsX-ANTsRCore-416d8f1/src/ants/Examples/ -I../inst/include/   -I/private/var/folders/74/6qb79c494tj_r61_vggqsvgh0000gp/T/Rtmpe8xnBk/devtools73e63aecbc58/ANTsX-ANTsRCore-416d8f1/src/ants/Tensor/  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ITKR/include" -I/usr/local/include   -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c Atropos.cpp -o Atropos.o
In file included from Atropos.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/usr/local/clang8/bin/../include/c++/v1/cmath:314:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/usr/local/clang8/bin/../include/c++/v1/cmath:315:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/usr/local/clang8/bin/../include/c++/v1/cmath:316:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
using ::isfinite;
      ~~^
...
ntustison commented 4 years ago

Okay, based on this thread over at the rstan forum, I'm getting further than I have before. As @muschellij2 , things have significantly changed due to Catalina. So this is my ~/.R/Makevars

CC=/usr/bin/clang
CXX=/usr/bin/clang++
CXX11=/usr/bin/clang++
CXX14=/usr/bin/clang++
CXX17=/usr/bin/clang++
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXX11FLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXX14FLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXX17FLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
FC=/usr/local/gfortran/bin/gfortran
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0  -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
LDFLAGS=-L/usr/local/clang8/lib -L/usr/local/lib
R_LD_LIBRARY_PATH=/usr/local/clang8/lib:/usr/local/lib

Currently getting a bunch of warnings (due to the compiler flags) but it's compiling further than it has before.

ntustison commented 4 years ago

Okay, this works for me. Thanks, gentlemen, for your help.

muschellij2 commented 4 years ago

Getting the same issues now with new ANTsRCore:

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:318:9: error: no member named 'signbit' in the global namespace
   using ::signbit;
         ~~^
Re-compiling ANTsRCore
─  installing *source* package ‘ANTsRCore’ ... (424ms)
   ** using staged installation
   Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
   darwin18 1
   Cloning into 'ants'...
Updating files: 100% (734/734), done.
   Already on 'master'
   Your branch is up to date with 'origin/master'.
   Already up to date.
   Note: switching to 'a025d042f56561812172a1f6b2ae6848ad914767'.

   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 switching back to a branch.

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

     git switch -c <new-branch-name>

   Or undo this operation with:

     git switch -

   Turn off this advice by setting config variable advice.detachedHead to false

   HEAD is now at a025d042 DOC: Update issue templates
   -- The C compiler identification is AppleClang 11.0.0.11000033
   -- The CXX compiler identification is AppleClang 11.0.0.11000033
   -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
   -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/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: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
   -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
   -- Detecting CXX compiler ABI info
   -- Detecting CXX compiler ABI info - done
   -- Detecting CXX compile features
   -- Detecting CXX compile features - done
   -- Using CCache
   -- 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-Wno-long-double
   -- Performing Test C_HAS_WARNING-Wno-long-double - Failed
   -- 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-Wno-long-double
   -- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed
   -- 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-Wno-undefined-var-template
   -- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - 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
   -- Performing Test C_HAS_WARNING-mtune_native
   -- Performing Test C_HAS_WARNING-mtune_native - Success
   -- Performing Test C_HAS_WARNING-march_corei7
   -- Performing Test C_HAS_WARNING-march_corei7 - Success
   -- Performing Test CXX_HAS_WARNING-mtune_native
   -- Performing Test CXX_HAS_WARNING-mtune_native - Success
   -- Performing Test CXX_HAS_WARNING-march_corei7
   -- Performing Test CXX_HAS_WARNING-march_corei7 - Success
   -- Found Git: /usr/local/bin/git (found version "2.24.1") 
   -- SuperBuild - ANTS => Requires ITKv5, 
   -- SuperBuild -   ITKv5[OK]
   -- SuperBuild - ANTS[OK]
   -- Configuring done
   -- Generating done
   CMake Warning:
     Manually-specified variables were not used by the project:

       COPY_SCRIPT_FILES_TO_BIN_DIR

   -- Build files have been written to: /Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/antb
   ** libs
   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-5.1/ -I/Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src -I/Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Examples/include/   -I/Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Utilities -I/Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Examples/ -I../inst/include/   -I/Users/johnmuschelli/Dropbox/Packages/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:4:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:318:9: error: no member named 'signbit' in the global namespace
   using ::signbit;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:319:9: error: no member named 'fpclassify' in the global namespace
   using ::fpclassify;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:320:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
   using ::isfinite;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/math.h:749:12: note: 'finite' declared here
   extern int finite(double)
              ^
   In file included from Atropos.cpp:4:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:321:9: error: no member named 'isinf' in the global namespace
   using ::isinf;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:322:9: error: no member named 'isnan' in the global namespace
   using ::isnan;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:323:9: error: no member named 'isnormal' in the global namespace
   using ::isnormal;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:324:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
   using ::isgreater;
         ^~
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/functional:728:29: note: '::std::greater' declared here
   struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                               ^
   In file included from Atropos.cpp:4:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:325:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
   using ::isgreaterequal;
         ^~
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/functional:757:29: note: '::std::greater_equal' declared here
   struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                               ^
   In file included from Atropos.cpp:4:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:326:9: error: no member named 'isless' in the global namespace
   using ::isless;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:327:9: error: no member named 'islessequal' in the global namespace
   using ::islessequal;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:328:9: error: no member named 'islessgreater' in the global namespace
   using ::islessgreater;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:329:9: error: no member named 'isunordered' in the global namespace
   using ::isunordered;
         ~~^
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:330:9: error: no member named 'isunordered' in the global namespace
   using ::isunordered;
         ~~^
   In file included from Atropos.cpp:5:
   In file included from /Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Examples/include/ants.h:4:
   In file included from /Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Utilities/itkSurfaceCurvatureBase.h:23:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkProcessObject.h:32:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkDomainThreader.h:22:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMultiThreaderBase.h:35:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageRegion.h:34:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkContinuousIndex.h:21:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkPoint.h:23:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.h:332:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.hxx:21:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:33:
   /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/vnl/vnl_math.h:199:15: error: expected unqualified-id
     inline bool isinf(TArg arg) { return bool(std::isinf(arg)); }
                 ^
   /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/math.h:160:7: note: expanded from macro 'isinf'
       ( sizeof(x) == sizeof(float)  ? __inline_isinff((float)(x))          \
         ^
   In file included from Atropos.cpp:5:
   In file included from /Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Examples/include/ants.h:4:
   In file included from /Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Utilities/itkSurfaceCurvatureBase.h:23:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkProcessObject.h:32:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkDomainThreader.h:22:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMultiThreaderBase.h:35:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageRegion.h:34:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkContinuousIndex.h:21:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkPoint.h:23:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.h:332:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.hxx:21:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:33:
   /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/vnl/vnl_math.h:199:15: error: expected ')'
   /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/math.h:160:7: note: expanded from macro 'isinf'
       ( sizeof(x) == sizeof(float)  ? __inline_isinff((float)(x))          \
         ^
   /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/vnl/vnl_math.h:199:15: note: to match this '('
   /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/math.h:160:5: note: expanded from macro 'isinf'
       ( sizeof(x) == sizeof(float)  ? __inline_isinff((float)(x))          \
       ^
   In file included from Atropos.cpp:5:
   In file included from /Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Examples/include/ants.h:4:
   In file included from /Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Utilities/itkSurfaceCurvatureBase.h:23:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkProcessObject.h:32:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkDomainThreader.h:22:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMultiThreaderBase.h:35:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageRegion.h:34:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkContinuousIndex.h:21:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkPoint.h:23:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.h:332:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.hxx:21:
   /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:770:12: error: no member named 'isnan' in namespace 'std'
   using std::isnan;
         ~~~~~^
   /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:771:12: error: no member named 'isinf' in namespace 'std'
   using std::isinf;
         ~~~~~^
   /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:772:12: error: no member named 'isfinite' in namespace 'std'; did you mean 'finite'?
   using std::isfinite;
         ~~~~~^~~~~~~~
              finite
   /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:320:9: note: 'finite' declared here
   using ::isfinite;
           ^
   In file included from Atropos.cpp:5:
   In file included from /Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Examples/include/ants.h:4:
   In file included from /Users/johnmuschelli/Dropbox/Packages/ANTsRCore/src/ants/Utilities/itkSurfaceCurvatureBase.h:23:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkProcessObject.h:32:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkDomainThreader.h:22:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMultiThreaderBase.h:35:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageRegion.h:34:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkContinuousIndex.h:21:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkPoint.h:23:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.h:332:
   In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkVector.hxx:21:
   /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkMath.h:773:12: error: no member named 'isnormal' in namespace 'std'
   using std::isnormal;
         ~~~~~^
   fatal error: too many errors emitted, stopping now [-ferror-limit=]
   20 errors generated.
   make: *** [Atropos.o] Error 1
   ERROR: compilation failed for package ‘ANTsRCore’
muschellij2 commented 4 years ago

Related to https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers-yield-error-no-member-named-signbit-in-th and https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with-c-code-after-updating-to-macos-catalina

muschellij2 commented 4 years ago

https://stackoverflow.com/a/58313170/2549133 indicates R 3.6.1 patched fixes this.

muschellij2 commented 4 years ago

May be a CMake thing: https://gitlab.kitware.com/cmake/cmake/issues/19845

muschellij2 commented 4 years ago

After I've had this issue with breaking installs all over the place, removing Xcode.App was the only thing that worked, from https://github.com/PointCloudLibrary/pcl/issues/2601#issuecomment-486889884

muschellij2 commented 3 years ago

After running into this over and over again, I think I can at least figure out a solution @cookpa: 1) I used Xcode vs. Command line tools. Shouldn't make a difference but it did. 2) I wiped out /usr/local/include. I had to remake it in case brew was mad. Not sure if this was a problem or not, but I did it. 3) Added -stdlib=libc++ to ~/.R/Makevars for C++ compiling. Here is my full output (relevant parts are at the end)

CCACHE=ccache
CC=$(CCACHE) clang
CXX=$(CCACHE) clang++
CXX11=$(CCACHE) clang++
CXX14=$(CCACHE) clang++
CXX17=$(CCACHE) clang++

SHLIB_OPENMP_CFLAGS=
SHLIB_OPENMP_CXXFLAGS=
SHLIB_OPENMP_CPPFLAGS=
SHLIB_OPENMP_FCFLAGS= 
SHLIB_OPENMP_FFLAGS=

CXXFLAGS=-stdlib=libc++
CXX11FLAGS=-stdlib=libc++
CXX14FLAGS=-stdlib=libc++
CXX17FLAGS=-stdlib=libc++
CXX20FLAGS=-stdlib=libc++
LDFLAGS=-stdlib=libc++

4) This allowed me to install rgl and I'm running ITK now as well.