View Revisions: Issue #4681

Summary 0004681: No /usr/include on macOS Mojave
Revision 2019-04-18 18:11 by jcfr
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 "setup.py", line 415, in <module>
    setup_package()
  File "setup.py", line 407, in setup_package
    setup(**metadata)
  File "/q5r/NUMPY/numpy/distutils/core.py", 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/__init__.py", line 145, in setup
    return distutils.core.setup(**attrs)
  File "/q5r/python-install/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/q5r/python-install/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/q5r/python-install/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/q5r/NUMPY/numpy/distutils/command/build.py", line 47, in run
    old_build.run(self)
  File "/q5r/python-install/lib/python2.7/distutils/command/build.py", line 127, in run
    self.run_command(cmd_name)
  File "/q5r/python-install/lib/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/q5r/python-install/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 148, in run
    self.build_sources()
  File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 165, in build_sources
    self.build_extension_sources(ext)
  File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 322, in build_extension_sources
    sources = self.generate_sources(sources, ext)
  File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 375, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/setup.py", line 423, in generate_config_h
    moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
  File "numpy/core/setup.py", line 47, in check_types
    out = check_types(*a, **kw)
  File "numpy/core/setup.py", 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
  /q5r/NUMPY_build_step_error.txt.

=======================================================================================

Revision 2019-04-18 18:11 by jcfr
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 "setup.py", line 415, in <module>
    setup_package()
  File "setup.py", line 407, in setup_package
    setup(**metadata)
  File "/q5r/NUMPY/numpy/distutils/core.py", 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/__init__.py", line 145, in setup
    return distutils.core.setup(**attrs)
  File "/q5r/python-install/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/q5r/python-install/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/q5r/python-install/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/q5r/NUMPY/numpy/distutils/command/build.py", line 47, in run
    old_build.run(self)
  File "/q5r/python-install/lib/python2.7/distutils/command/build.py", line 127, in run
    self.run_command(cmd_name)
  File "/q5r/python-install/lib/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/q5r/python-install/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 148, in run
    self.build_sources()
  File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 165, in build_sources
    self.build_extension_sources(ext)
  File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 322, in build_extension_sources
    sources = self.generate_sources(sources, ext)
  File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 375, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/setup.py", line 423, in generate_config_h
    moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
  File "numpy/core/setup.py", line 47, in check_types
    out = check_types(*a, **kw)
  File "numpy/core/setup.py", 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
  /q5r/NUMPY_build_step_error.txt.

=======================================================================================

Revision 2019-03-29 21:07 by pieper
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 "setup.py", line 415, in <module>
setup_package()
File "setup.py", line 407, in setup_package
setup(metadata)
File "/q5r/NUMPY/numpy/distutils/core.py", 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/init.py", line 145, in setup
return distutils.core.setup(*attrs)
File "/q5r/python-install/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/q5r/python-install/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/q5r/python-install/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/q5r/NUMPY/numpy/distutils/command/build.py", line 47, in run
old_build.run(self)
File "/q5r/python-install/lib/python2.7/distutils/command/build.py", line 127, in run
self.run_command(cmd_name)
File "/q5r/python-install/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/q5r/python-install/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 148, in run
self.build_sources()
File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 165, in build_sources
self.build_extension_sources(ext)
File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 322, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/q5r/NUMPY/numpy/distutils/command/build_src.py", line 375, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 423, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 47, in check_types
out = check_types(
a, **kw)
File "numpy/core/setup.py", 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
/q5r/NUMPY_build_step_error.txt.

=======================================================================================