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IDProjectCategoryView StatusLast Update
0004681Slicer4Core: Building (CMake, Superbuild)public2019-05-07 13:44
ReporterpieperAssigned Tojcfr 
Status assignedResolutionopen 
Product VersionSlicer 4.11.0 
Target VersionSlicer 4.11.0Fixed in Version 
Summary0004681: No /usr/include on macOS Mojave

It seems that with macOS 10.14 and beyond, Apple is deprecating the use of /usr/include and instead puts the corresponding files in the os-version-specific SDK directories:

(note that xcode-select --install does not fix this)

This breaks OpenSSL and Python with the errors shown in Additional Information below. Probably other things break too.

A workaround is setting the SDKROOT, like this, which allows the build to succeed:

SDKROOT=/Applications/ make -j20

We should find a way to send the correct SDKROOT to the SuperBuild dependencies, e.g. via cmake as a byproduct of setting the CMAKE_OSX_DEPLOYMENT_TARGET.

Additional Information

build error compiling OpenSSL

[ 20%] Performing update step for 'zlib'
[ 20%] Performing configure step for 'zlib'
loading initial cache file /q5r/zlib-prefix/tmp/zlib-cache-Debug.cmake
-- Configuring done
-- Generating done
-- Build files have been written to: /q5r/zlib-build
[ 20%] Performing build step for 'zlib'
[100%] Built target zlib
[ 20%] Performing install step for 'zlib'
[100%] Built target zlib
Install the project...
-- Install configuration: "Debug"
-- Up-to-date: /q5r/zlib-install/lib/libzlib.a
-- Up-to-date: /q5r/zlib-install/include/zlib.h
-- Up-to-date: /q5r/zlib-install/include/zconf.h
-- Up-to-date: /q5r/zlib-install/include/zlib_mangle.h
-- Up-to-date: /q5r/zlib-install/include/zlibDllConfig.h
-- Up-to-date: /q5r/zlib-install/doc/zlib-1.2.3/Copyright.txt
[ 40%] Completed 'zlib'
[ 60%] Built target zlib
[ 60%] No configure step for 'OpenSSL'
[ 60%] Performing build step for 'OpenSSL'
making all in crypto...
In file included from cryptlib.c:117:
./cryptlib.h:62:11: fatal error: 'stdlib.h' file not found
# include <stdlib.h>
1 error generated.
make[5]: *** [cryptlib.o] Error 1
make[4]: *** [build_crypto] Error 1
make[3]: *** [OpenSSL-prefix/src/OpenSSL-stamp/OpenSSL-build] Error 2
make[2]: *** [CMakeFiles/OpenSSL.dir/all] Error 2
make[1]: *** [CMakeFiles/OpenSSL.dir/rule] Error 2
make: *** [OpenSSL] Error 2

later, after setting SDKROOT and compiling Python

In file included from _configtest.c:1:
/q5r/python-install/include/python2.7/Python.h:33:10: fatal error: 'stdio.h' file not found
#include <stdio.h>
1 error generated.
Traceback (most recent call last):
  File "", line 415, in <module>
  File "", line 407, in setup_package
  File "/q5r/NUMPY/numpy/distutils/", line 171, in setup
    return old_setup(**new_attr)
  File "/q5r/python-install/lib/python2.7/site-packages/setuptools-40.8.0.post20190329-py2.7.egg/setuptools/", line 145, in setup
    return distutils.core.setup(**attrs)
  File "/q5r/python-install/lib/python2.7/distutils/", line 151, in setup
  File "/q5r/python-install/lib/python2.7/distutils/", line 953, in run_commands
  File "/q5r/python-install/lib/python2.7/distutils/", line 972, in run_command
  File "/q5r/NUMPY/numpy/distutils/command/", line 47, in run
  File "/q5r/python-install/lib/python2.7/distutils/command/", line 127, in run
  File "/q5r/python-install/lib/python2.7/distutils/", line 326, in run_command
  File "/q5r/python-install/lib/python2.7/distutils/", line 972, in run_command
  File "/q5r/NUMPY/numpy/distutils/command/", line 148, in run
  File "/q5r/NUMPY/numpy/distutils/command/", line 165, in build_sources
  File "/q5r/NUMPY/numpy/distutils/command/", line 322, in build_extension_sources
    sources = self.generate_sources(sources, ext)
  File "/q5r/NUMPY/numpy/distutils/command/", line 375, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/", line 423, in generate_config_h
    moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
  File "numpy/core/", line 47, in check_types
    out = check_types(*a, **kw)
  File "numpy/core/", line 281, in check_types
    "install {0}-dev|{0}-devel.".format(python))
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

CMake Error at /Users/pieper/slicer4/latest/Slicer/CMake/ExternalProjectForNonCMakeProject.cmake:104 (message):
  NUMPY: build step failed with exit code '1'.

  Outputs also captured in /q5r/NUMPY_build_step_output.txt and


TagsNo tags attached.




2019-03-29 21:08

administrator   ~0016253

Reminder sent to: jcfr

@jcfr - would be happy to hear your thoughts on this.



2019-05-07 13:44

administrator   ~0016258

On a recent rebuild this error showed up in the Swig_build/config.log. Setting the SDK environment variable as reported above gets past this.

Issue History

Date Modified Username Field Change
2019-03-29 21:07 pieper New Issue
2019-03-29 21:07 pieper Status new => assigned
2019-03-29 21:07 pieper Assigned To => jcfr
2019-03-29 21:08 pieper Note Added: 0016253
2019-04-18 18:11 jcfr Additional Information Updated View Revisions
2019-04-18 18:11 jcfr Additional Information Updated View Revisions
2019-04-30 15:41 jcfr Target Version Slicer 4.10.2 => Slicer 4.11.0
2019-05-07 13:44 pieper Note Added: 0016258