Compilation issue including ITK with brew on MacOS

Ber · December 17, 2021, 2:26pm

Hi ITK teams,
We get an issue once using ITK (5.2.1) through brew and macOs and obtain this type of error related to cmath use:
Applications/Xcode_13.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.0.sdk/usr/include/c++/v1/cmath:321:9: error: no member named ‘signbit’ in the global namespace

See more details here from githubaction compilation issue: work space · kerautret/ITKtestBrewGithubActions@8413eeb · GitHub

It looks related to the use of ITK since not using it and using cmath.h does not provides any errors:

Did you have an idea of fix ? (without switching of MacOS SDK that is not always possible).

phcerdan · December 17, 2021, 2:49pm

HI @Ber, not a MacOS user here, but isn’t this related to homebrew? Maybe a missmatch between the SDK used by homebrew and yours? Not sure.

For reference, links to formula in homebrew and their std_cmake_args handling SDK:

github.com

Homebrew/homebrew-core/blob/HEAD/Formula/itk.rb

class Itk < Formula
  desc "Insight Toolkit is a toolkit for performing registration and segmentation"
  homepage "https://itk.org"
  url "https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.2.1/InsightToolkit-5.2.1.tar.gz"
  sha256 "192d41bcdd258273d88069094f98c61c38693553fd751b54f8cda308439555db"
  license "Apache-2.0"
  head "https://github.com/InsightSoftwareConsortium/ITK.git"

  livecheck do
    url :stable
    regex(/^v?(\d+(?:\.\d+)+)$/i)
  end

  bottle do
    sha256 arm64_big_sur: "7b59055f5a4d15929975183ff03593a0500f6f9a4ff70d740ab184b29e182b99"
    sha256 big_sur:       "b7b30cd49b92cfcbd05404a4d0a592f3623f122354a82e458d5ee01ac2f9aa73"
    sha256 catalina:      "2e87abe07201cd013ac9535b02f3a012e79b049327d5ecc6ff015b1752c0a7f8"
    sha256 mojave:        "d2020a7710d5b42d0d833ff04ee2d821ff8080f34c8d2d00a86feaa39f6dfa25"
    sha256 x86_64_linux:  "c848dd47f4c45a3def027fac4d9b640f554ceb3ef97e35e6f2d45b3e44f8a73c"
  end

This file has been truncated. show original

github.com

Homebrew/brew/blob/master/Library/Homebrew/formula.rb#L1515-L1534

    
      
          def std_cmake_args(install_prefix: prefix, install_libdir: "lib", find_framework: "LAST")
            args = %W[
              -DCMAKE_INSTALL_PREFIX=#{install_prefix}
              -DCMAKE_INSTALL_LIBDIR=#{install_libdir}
              -DCMAKE_BUILD_TYPE=Release
              -DCMAKE_FIND_FRAMEWORK=#{find_framework}
              -DCMAKE_VERBOSE_MAKEFILE=ON
              -Wno-dev
              -DBUILD_TESTING=OFF
            ]
          
          
  # Avoid false positives for clock_gettime support on 10.11.
            # CMake cache entries for other weak symbols may be added here as needed.
            args << "-DHAVE_CLOCK_GETTIME:INTERNAL=0" if MacOS.version == "10.11" && MacOS::Xcode.version >= "8.0"
          
          
  # Ensure CMake is using the same SDK we are using.
            args << "-DCMAKE_OSX_SYSROOT=#{MacOS.sdk_for_formula(self).path}" if MacOS.sdk_root_needed?
          
          
  args
          end

Ber · December 18, 2021, 9:53am

Hi Pablo!
Thanks for your suggestions. Yes probably since when using the command line tools SDK it compiles, I tried to edit the formula and adding an cmake option: -DCMAKE_OSX_SYSROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
but I get compilations errors on itkv3p_netlib (while it works from full manual installation from source from default).

Ber · December 18, 2021, 10:35am

A possible workaround to successfully compile without using Xcode-select is just to add an cmake option: set(CMAKE_OSX_SYSROOT “/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk”)
That looks to be fine and do not change the user global config:

Ber · December 18, 2021, 12:21pm

I get also some fiftw used by ITK when using CMAKE_OSX_SYSROOT option: