Errors building python_example from pybind11 docs on macos - macos

Question

I get compiler errors when following the instructions from the pybind11 docs for the example build housed at https://github.com/pybind/python_example
The instructions are (1) clone the repo, and (2) pip3 install ./python_example.
I'm on OS X (Mojave) with python 3.7.3 and
c++ --version
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
I'm very new to python packages and to pybind11, so I'm more than a little lost and would appreciate newbie guidance. It looks like the errors have to do with implementations for C++ operator new and delete.
If so, I'm confident that I'm not the first person to have this issue and would appreciate a pointer to a solution.
I followed the steps given on the github repo:
Cloning into 'python_example'...
remote: Enumerating objects: 13, done.
remote: Counting objects: 100% (13/13), done.
remote: Compressing objects: 100% (9/9), done.
remote: Total 132 (delta 4), reused 11 (delta 4), pack-reused 119
Receiving objects: 100% (132/132), 31.03 KiB | 373.00 KiB/s, done.
Resolving deltas: 100% (62/62), done.
$ pip3 install ./python_example/
Here is the full output. Is something in the repo misconfigured (I did no configuration)? Is this a python version thing? A missing compiler flag? If I distribute code using this setup as a template, is there anything I need to do to increase portability? I'm a little worried that the "hello world" example has me on stack overflow! Thanks in advance for any help.
Processing ./python_example
Requirement already satisfied: pybind11>=2.3 in /usr/local/lib/python3.7/site-packages (from python-example==0.0.1) (2.3.0)
Building wheels for collected packages: python-example
Building wheel for python-example (setup.py) ... error
Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/pip-req-build-9f8udd0w/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /private/var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/pip-wheel-fk0w8_oq --python-tag cp37:
running bdist_wheel
running build
running build_ext
creating var
creating var/folders
creating var/folders/7l
creating var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn
creating var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c /var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/tmpag19sot6.cpp -o var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/tmpag19sot6.o -std=c++17
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c /var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/tmpf327436e.cpp -o var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/tmpf327436e.o -fvisibility=hidden
building 'python_example' extension
creating build
creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/src
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include/python3.7m -I/Users/stevescott/Library/Python/3.7/include/python3.7m -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c src/main.cpp -o build/temp.macosx-10.14-x86_64-3.7/src/main.o -stdlib=libc++ -mmacosx-version-min=10.7 -DVERSION_INFO="0.0.1" -std=c++17 -fvisibility=hidden
In file included from src/main.cpp:1:
In file included from /usr/local/include/python3.7m/pybind11/pybind11.h:49:
In file included from /usr/local/include/python3.7m/pybind11/attr.h:13:
/usr/local/include/python3.7m/pybind11/cast.h:579:34: error: aligned allocation function of type 'void *(unsigned long, enum std::align_val_t)' is only available on macOS 10.14 or newer
vptr = ::operator new(type->type_size,
^
/usr/local/include/python3.7m/pybind11/cast.h:579:34: note: if you supply your own aligned allocation functions, use -faligned-allocation to silence this diagnostic
In file included from src/main.cpp:1:
/usr/local/include/python3.7m/pybind11/pybind11.h:1009:9: error: no matching function for call to 'operator delete'
::operator delete(p, s, std::align_val_t(a));
^~~~~~~~~~~~~~~~~
note: candidate function not viable: requires 2 arguments, but 3 were provided
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:188:36: note: candidate function not viable: requires 2 arguments, but 3 were provided
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p, const std::nothrow_t&) _NOEXCEPT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:190:74: note: candidate function not viable: requires 2 arguments, but 3 were provided
_LIBCPP_OVERRIDABLE_FUNC_VIS _LIBCPP_AVAILABILITY_SIZED_NEW_DELETE void operator delete(void* __p, std::size_t __sz) _NOEXCEPT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:221:40: note: candidate function not viable: requires 2 arguments, but 3 were provided
inline _LIBCPP_INLINE_VISIBILITY void operator delete (void*, void*) _NOEXCEPT {}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:187:36: note: candidate function not viable: requires single argument '__p', but 3 arguments were provided
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p) _NOEXCEPT;
^
In file included from src/main.cpp:1:
/usr/local/include/python3.7m/pybind11/pybind11.h:1011:9: error: call to unavailable function 'operator delete': introduced in macOS 10.12
::operator delete(p, s);
^~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:190:74: note: candidate function has been explicitly made unavailable
_LIBCPP_OVERRIDABLE_FUNC_VIS _LIBCPP_AVAILABILITY_SIZED_NEW_DELETE void operator delete(void* __p, std::size_t __sz) _NOEXCEPT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:221:40: note: candidate function not viable: no known conversion from 'pybind11::size_t' (aka 'unsigned long') to 'void *' for 2nd argument; take the address of the argument with &
inline _LIBCPP_INLINE_VISIBILITY void operator delete (void*, void*) _NOEXCEPT {}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:188:36: note: candidate function not viable: no known conversion from 'pybind11::size_t' (aka 'unsigned long') to 'const std::nothrow_t' for 2nd argument
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p, const std::nothrow_t&) _NOEXCEPT;
^
note: candidate function not viable: no known conversion from 'pybind11::size_t' (aka 'unsigned long') to 'std::align_val_t' for 2nd argument
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:187:36: note: candidate function not viable: requires single argument '__p', but 2 arguments were provided
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p) _NOEXCEPT;
^
3 errors generated.
error: command 'clang' failed with exit status 1
----------------------------------------
Failed building wheel for python-example
Running setup.py clean for python-example
Failed to build python-example
Installing collected packages: python-example
Running setup.py install for python-example ... error
Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/pip-req-build-9f8udd0w/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/pip-record-yvb3nloo/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_ext
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c /var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/tmpkd6a1ugc.cpp -o var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/tmpkd6a1ugc.o -std=c++17
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c /var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/tmpywf858_h.cpp -o var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/tmpywf858_h.o -fvisibility=hidden
building 'python_example' extension
creating build
creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/src
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include/python3.7m -I/Users/stevescott/Library/Python/3.7/include/python3.7m -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c src/main.cpp -o build/temp.macosx-10.14-x86_64-3.7/src/main.o -stdlib=libc++ -mmacosx-version-min=10.7 -DVERSION_INFO="0.0.1" -std=c++17 -fvisibility=hidden
In file included from src/main.cpp:1:
In file included from /usr/local/include/python3.7m/pybind11/pybind11.h:49:
In file included from /usr/local/include/python3.7m/pybind11/attr.h:13:
/usr/local/include/python3.7m/pybind11/cast.h:579:34: error: aligned allocation function of type 'void *(unsigned long, enum std::align_val_t)' is only available on macOS 10.14 or newer
vptr = ::operator new(type->type_size,
^
/usr/local/include/python3.7m/pybind11/cast.h:579:34: note: if you supply your own aligned allocation functions, use -faligned-allocation to silence this diagnostic
In file included from src/main.cpp:1:
/usr/local/include/python3.7m/pybind11/pybind11.h:1009:9: error: no matching function for call to 'operator delete'
::operator delete(p, s, std::align_val_t(a));
^~~~~~~~~~~~~~~~~
note: candidate function not viable: requires 2 arguments, but 3 were provided
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:188:36: note: candidate function not viable: requires 2 arguments, but 3 were provided
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p, const std::nothrow_t&) _NOEXCEPT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:190:74: note: candidate function not viable: requires 2 arguments, but 3 were provided
_LIBCPP_OVERRIDABLE_FUNC_VIS _LIBCPP_AVAILABILITY_SIZED_NEW_DELETE void operator delete(void* __p, std::size_t __sz) _NOEXCEPT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:221:40: note: candidate function not viable: requires 2 arguments, but 3 were provided
inline _LIBCPP_INLINE_VISIBILITY void operator delete (void*, void*) _NOEXCEPT {}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:187:36: note: candidate function not viable: requires single argument '__p', but 3 arguments were provided
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p) _NOEXCEPT;
^
In file included from src/main.cpp:1:
/usr/local/include/python3.7m/pybind11/pybind11.h:1011:9: error: call to unavailable function 'operator delete': introduced in macOS 10.12
::operator delete(p, s);
^~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:190:74: note: candidate function has been explicitly made unavailable
_LIBCPP_OVERRIDABLE_FUNC_VIS _LIBCPP_AVAILABILITY_SIZED_NEW_DELETE void operator delete(void* __p, std::size_t __sz) _NOEXCEPT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:221:40: note: candidate function not viable: no known conversion from 'pybind11::size_t' (aka 'unsigned long') to 'void *' for 2nd argument; take the address of the argument with &
inline _LIBCPP_INLINE_VISIBILITY void operator delete (void*, void*) _NOEXCEPT {}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:188:36: note: candidate function not viable: no known conversion from 'pybind11::size_t' (aka 'unsigned long') to 'const std::nothrow_t' for 2nd argument
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p, const std::nothrow_t&) _NOEXCEPT;
^
note: candidate function not viable: no known conversion from 'pybind11::size_t' (aka 'unsigned long') to 'std::align_val_t' for 2nd argument
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/new:187:36: note: candidate function not viable: requires single argument '__p', but 2 arguments were provided
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p) _NOEXCEPT;
^
3 errors generated.
error: command 'clang' failed with exit status 1
----------------------------------------
Command "/usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/pip-req-build-9f8udd0w/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/pip-record-yvb3nloo/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/7l/5r4qgkms4vb3xm6ktxdvh1l80000gn/T/pip-req-build-9f8udd0w/

Answer 1

I ran into the same issue with my pybind11 project on Mac OS.
I haven't been able to figure it out the root cause, but found a workaround: I disabled the C++17 cpp flag by removing the -std=c++17 from the list here.
Therefore instead of receiving the same errors that you mentioned, I got them as warnings. It's not a proper solution, and I really like to see a real explanation for this, but at least I have my source code compiled.
Update:
As eudoxos pointed out in his comment they opened an issue on pybind11's github page related to this and the fix should be in the next release.