No /usr/include on macOS Mojave #4681

slicerbot · 2020-03-13T01:05:06Z

This issue was created automatically from an original Mantis Issue. Further discussion may take place here.

pieper · 2020-03-26T17:52:48Z

@Slicer/slicer-developer does anyone have an idea how best to fix this? To me this seems like something to fix at the CMake level, but I guess we could just set the environment variable as part of our build.

ihnorton · 2020-03-26T18:41:57Z

Update this to use/require CMAKE_OSX_SYSROOT instead of CMAKE_OSX_DEPLOYMENT_TARGET? Not clear to me if ExternalProject_Add automatically passes that down to the sub-project (it is not currently passed through by Slicer AFAICT).

jcfr · 2020-03-26T18:49:10Z

Since:

numpy is now installed from a wheel, the numpy build problem reported in the original is obselete.
this issue affect only non CMake project. Indeed, having CMAKE_OSX_SYSROOT set is sufficient for CMake project.

Could you test the following patch:

diff --git a/CMake/ExternalProjectForNonCMakeProject.cmake b/CMake/ExternalProjectForNonCMakeProject.cmake
index efafbdfa75..a316cb30bd 100644
--- a/CMake/ExternalProjectForNonCMakeProject.cmake
+++ b/CMake/ExternalProjectForNonCMakeProject.cmake
@@ -215,6 +215,10 @@ if(APPLE)
   endif()
   set(CMAKE_OSX_FLAGS \"\${osx_arch_flags} \${osx_version_flag} \${osx_sysroot}\")
 
+  if(NOT DEFINED ENV{SDKROOT})
+    set(ENV{SDKROOT} \"\${CMAKE_OSX_SYSROOT}\")
+  endif()
+
   _ep_var_append(_ep_CFLAGS \"\${CMAKE_OSX_FLAGS}\")
   _ep_var_append(_ep_CXXFLAGS \"\${CMAKE_OSX_FLAGS}\")
   _ep_var_append(_ep_LDFLAGS \"\${CMAKE_OSX_FLAGS}\")

@pieper Based on your feedback, I will then submit a PR.

pieper · 2020-04-20T16:13:16Z

@jcfr Just tried applying that patch but it didn't solve the problem. Probably it sets the environment of the wrong process.

It seems like we need to add the variable in OpenSSL_Env.cmake. Is that generated in our SuperBuild or somewhere in CMake?

CMake computes the value of the -isysroot flag for cmake builds. OpenSSL does not have a mechanism for setting this directly, so using an environmental variable allows the compiler to pick up the correct SDKROOT path. Allow the SDKROOT to be found on mac when building OpenSSL. This is needed to find standard header files and avoid errors like ``` ./cryptlib.h:62:11: fatal error: 'stdlib.h' file not found # include <stdlib.h> ``` Related to Slicer#4681

jcfr · 2020-04-21T04:38:00Z

@pieper Thanks for testing

@hjmjohnson Thanks for working on a patch (for reference #4857)

It seems like we need to add the variable in OpenSSL_Env.cmake. Is that generated in our SuperBuild or somewhere in CMake?

Yes, and the proposed patch was intended to have the value set in that script. The problem was that the build command is not using a CMake wrapper script (and not including OpenSSL_Env.cmake

CMake computes the value of the -isysroot flag for cmake builds. OpenSSL does not have a mechanism for setting this directly, so using an environmental variable allows the compiler to pick up the correct SDKROOT path. Allow the SDKROOT to be found on mac when building OpenSSL. This is needed to find standard header files and avoid errors like ``` ./cryptlib.h:62:11: fatal error: 'stdlib.h' file not found # include <stdlib.h> ``` Related to Slicer#4681

CMake computes the value of the -isysroot flag for cmake builds. OpenSSL does not have a mechanism for setting this directly, so using an environmental variable allows the compiler to pick up the correct SDKROOT path. Allow the SDKROOT to be found on mac when building OpenSSL. This is needed to find standard header files and avoid errors like ``` ./cryptlib.h:62:11: fatal error: 'stdlib.h' file not found # include <stdlib.h> ``` Related to #4681

This commit fixes a regression introduced in ddeb0a3 (COMP: Fix OpenSSL build on Mac 10.15 XCode 11.4.1 (Slicer#4857)) originally intended to fix issue Slicer#4681 Setting the SDKROOT environment variable worked as expected on a regular developer build but failed on a dashboard build where the invocation of "make" is wrapped using a "launcher" [1] This commit addresses the issue by writing a CMake script that will set the environment and then invoke make. Last, since file descriptors expect by the make jobserver are not kept open by the CMake process, the build script explicitly unset MAKEFLAGS to avoid "warning: -jN forced in submake: disabling jobserver mode." For more details, see [2] [1] https://cmake.org/cmake/help/latest/manual/ctest.1.html#ctest-build-step [2] https://stackoverflow.com/questions/29910944/is-it-possible-to-pass-through-gnu-make-jobserver-environment-to-a-submake-ser

This commit fixes a regression introduced in ddeb0a3 (COMP: Fix OpenSSL build on Mac 10.15 XCode 11.4.1 (#4857)) originally intended to fix issue #4681 Setting the SDKROOT environment variable worked as expected on a regular developer build but failed on a dashboard build where the invocation of "make" is wrapped using a "launcher" [1] This commit addresses the issue by writing a CMake script that will set the environment and then invoke make. Last, since file descriptors expect by the make jobserver are not kept open by the CMake process, the build script explicitly unset MAKEFLAGS to avoid "warning: -jN forced in submake: disabling jobserver mode." For more details, see [2] [1] https://cmake.org/cmake/help/latest/manual/ctest.1.html#ctest-build-step [2] https://stackoverflow.com/questions/29910944/is-it-possible-to-pass-through-gnu-make-jobserver-environment-to-a-submake-ser

jamesobutler · 2020-06-05T11:24:34Z

Can this issue be closed? Is there any work that still needs to be done following all the referenced commits and PRs?

pieper · 2020-06-05T14:11:38Z

Yes, it seems to be working now. I no longer need to specify the path on the command line.

On mac I currently configure with the script below.

buildType=Debug
qtVersion=5.14

cmake \
	-DCMAKE_BUILD_TYPE:STRING=${buildType} \
	-DQt5_VERSION:STRING=${qtVersion} \
	-DSlicer_REQUIRED_QT_VERSION:STRING=${qtVersion} \
	-DQt5_DIR:PATH=/usr/local/opt/qt5/lib/cmake/Qt5 \
	-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.14 \
	/Users/pieper/slicer/latest/Slicer

slicerbot added this to the Slicer 4.11.0 milestone Mar 13, 2020

lassoan assigned pieper Mar 26, 2020

pieper mentioned this issue Apr 20, 2020

Fix OpenSSL build issues on Mac 10.15 XCode 11 clean OS #4857

Merged

jcfr linked a pull request Apr 23, 2020 that will close this issue

Fix OpenSSL build issues on Mac 10.15 XCode 11 clean OS #4857

Merged

jcfr mentioned this issue Apr 23, 2020

COMP: Fix OpenSSL build on macOS setting SDKROOT in build script #4883

Merged

jcfr linked a pull request Apr 23, 2020 that will close this issue

COMP: Fix OpenSSL build on macOS setting SDKROOT in build script #4883

Merged

pieper closed this as completed Jun 5, 2020

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No /usr/include on macOS Mojave #4681

No /usr/include on macOS Mojave #4681

slicerbot commented Mar 13, 2020

pieper commented Mar 26, 2020

ihnorton commented Mar 26, 2020

jcfr commented Mar 26, 2020 •

edited

pieper commented Apr 20, 2020

jcfr commented Apr 21, 2020 •

edited

jamesobutler commented Jun 5, 2020

pieper commented Jun 5, 2020 •

edited

No /usr/include on macOS Mojave #4681

No /usr/include on macOS Mojave #4681

Comments

slicerbot commented Mar 13, 2020

pieper commented Mar 26, 2020

ihnorton commented Mar 26, 2020

jcfr commented Mar 26, 2020 • edited

pieper commented Apr 20, 2020

jcfr commented Apr 21, 2020 • edited

jamesobutler commented Jun 5, 2020

pieper commented Jun 5, 2020 • edited

jcfr commented Mar 26, 2020 •

edited

jcfr commented Apr 21, 2020 •

edited

pieper commented Jun 5, 2020 •

edited