install issue on Fedora 39

[mosqueteer]

I could not install (nor build) point-cloud-utils (PCU) on fedora 39 + python 13.2.3 (and C++ 13.2.1).

I've got the following output after typing "sudo pip install ." to build PCU in the PCU's root directory:

Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in /usr/lib64/python3.12/site-packages (from point-cloud-utils==0.30.4) (1.24.4)
Collecting scipy (from point-cloud-utils==0.30.4)
Obtaining dependency information for scipy from https://files.pythonhosted.org/packages/88/ab/6ecdc526d509d33814835447bbbeedbebdec7cca46ef495a61b00a35b4bf/scipy-1.13.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
Using cached scipy-1.13.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Using cached scipy-1.13.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.2 MB)
Building wheels for collected packages: point-cloud-utils
Building wheel for point-cloud-utils (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for point-cloud-utils (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [322 lines of output]
running bdist_wheel
running build
running build_py
running build_ext
-- The C compiler identification is GNU 13.2.1
-- The CXX compiler identification is GNU 13.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.

    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  Cloning into 'numpyeigen'...
  Already on 'master'
  CMake Deprecation Warning at external/numpyeigen/cmake/numpyeigen.cmake:22 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
  Call Stack (most recent call first):
    CMakeLists.txt:40 (include)
 
 
  CMake Warning (dev) at external/numpyeigen/cmake/numpyeigen.cmake:98 (set):
    Cannot set "NPE_ROOT_DIR": current scope has no parent.
  Call Stack (most recent call first):
    CMakeLists.txt:40 (include)
  This warning is for project developers.  Use -Wno-dev to suppress it.
 
  CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  Cloning into 'eigen'...
  Switched to a new branch '3.4'
  CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  Cloning into 'pybind11'...
  Switched to a new branch 'new_numpy_hacks_stable'
  CMake Deprecation Warning at external/numpyeigen/external/pybind11/CMakeLists.txt:8 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  -- pybind11 v2.11.0 dev1
  CMake Warning (dev) at external/numpyeigen/external/pybind11/tools/FindPythonLibsNew.cmake:98 (find_package):
    Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
    are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
    the cmake_policy command to set the policy and suppress this warning.
 
  Call Stack (most recent call first):
    external/numpyeigen/external/pybind11/tools/pybind11Tools.cmake:50 (find_package)
    external/numpyeigen/external/pybind11/tools/pybind11Common.cmake:180 (include)
    external/numpyeigen/external/pybind11/CMakeLists.txt:210 (include)
  This warning is for project developers.  Use -Wno-dev to suppress it.
 
  -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.12.3", minimum required is "3.6")
  -- Found PythonLibs: PYTHON_LIBRARY-NOTFOUND
  CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  Cloning into 'igl'...
  HEAD is now at 68684132 adj list fix unref; manifold doc; icosa; tests (#2276) [ci skip]
  CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  Cloning into 'tinyply'...
  Switched to a new branch '2.4'
  CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  Cloning into 'tinyobjloader'...
  Already on 'release'
  CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  Cloning into 'manifold'...
  HEAD is now at 28e335f fix memory leak
  CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  Cloning into 'embree'...
  HEAD is now at 698442324 regenerated documentation
  CMake Deprecation Warning at external/embree/CMakeLists.txt:15 (CMAKE_MINIMUM_REQUIRED):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  -- GNU detected
  -- Detecting default ISA...
  -- Detected default ISA: SSE2
  CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  Cloning into 'geogram'...
  Already on 'main'
  CMake Deprecation Warning at external/geogram/CMakeLists.txt:9 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  -- Using local options file: /home/abelgomes/point-cloud-utils-master/external/geogram/CMakeOptions.txt
  -- Configuring build for standalone Geogram (without Vorpaline)
  -- GCC version >= 4.3, activating sign conversion warnings
  -- GCC version >= 4.6, activating double promotion warnings
  CMake Deprecation Warning at external/geogram/doc/CMakeLists.txt:7 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  -- Found OpenMP_C: -fopenmp (found version "4.5")
  -- Found OpenMP_CXX: -fopenmp (found version "4.5")
  -- Found OpenMP_C: -fopenmp (found version "4.5")
  -- Found OpenMP_CXX: -fopenmp (found version "4.5")
  CMake Deprecation Warning at tests/CMakeLists.txt:1 (cmake_minimum_required):
    Compatibility with CMake < 3.5 will be removed from a future version of
    CMake.
 
    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
 
 
  -- Configuring done (63.2s)
  -- Generating done (0.1s)
  -- Build files have been written to: /home/abelgomes/point-cloud-utils-master/build/temp.linux-x86_64-cpython-312
  [  1%] Building CXX object CMakeFiles/npe.dir/external/numpyeigen/src/npe_typedefs.cpp.o
  [  1%] Building CXX object CMakeFiles/manifold.dir/external/manifold/src/BVH.cpp.o
  <command-line>: warning: missing terminating " character
  <command-line>: warning: "VERSION_INFO" redefined
  <command-line>: note: this is the location of the previous definition
  In file included from /home/abelgomes/point-cloud-utils-master/external/numpyeigen/external/pybind11/include/pybind11/attr.h:13,
                   from /home/abelgomes/point-cloud-utils-master/external/numpyeigen/external/pybind11/include/pybind11/detail/class.h:12,
                   from /home/abelgomes/point-cloud-utils-master/external/numpyeigen/external/pybind11/include/pybind11/pybind11.h:13,
                   from /home/abelgomes/point-cloud-utils-master/external/numpyeigen/cmake/../src/npe_sparse_array.h:4,
                   from /home/abelgomes/point-cloud-utils-master/external/numpyeigen/src/npe_typedefs.h:6,
                   from /home/abelgomes/point-cloud-utils-master/external/numpyeigen/src/npe_typedefs.cpp:1:
  /home/abelgomes/point-cloud-utils-master/external/numpyeigen/external/pybind11/include/pybind11/detail/common.h:266:10: fatal error: Python.h: No such file or directory
    266 | #include <Python.h>
        |          ^~~~~~~~~~
  compilation terminated.
  gmake[2]: *** [CMakeFiles/npe.dir/build.make:76: CMakeFiles/npe.dir/external/numpyeigen/src/npe_typedefs.cpp.o] Error 1
  gmake[1]: *** [CMakeFiles/Makefile2:349: CMakeFiles/npe.dir/all] Error 2
  gmake[1]: *** Waiting for unfinished jobs....
  [  2%] Building CXX object CMakeFiles/manifold.dir/external/manifold/src/Intersection.cpp.o
  <command-line>: warning: missing terminating " character
  <command-line>: warning: "VERSION_INFO" redefined
  <command-line>: note: this is the location of the previous definition
  [  2%] Building CXX object CMakeFiles/manifold.dir/external/manifold/src/main.cpp.o
  <command-line>: warning: missing terminating " character
  <command-line>: warning: "VERSION_INFO" redefined
  <command-line>: note: this is the location of the previous definition
  [  2%] Building CXX object CMakeFiles/manifold.dir/external/manifold/src/Model_OBJ.cpp.o
  <command-line>: warning: missing terminating " character
  <command-line>: warning: "VERSION_INFO" redefined
  <command-line>: note: this is the location of the previous definition
  In file included from /home/abelgomes/point-cloud-utils-master/external/manifold/3rd/Eigen/Core:405,
                   from /home/abelgomes/point-cloud-utils-master/external/manifold/3rd/igl/readOBJ.h:18,
                   from /home/abelgomes/point-cloud-utils-master/external/manifold/src/Model_OBJ.h:20,
                   from /home/abelgomes/point-cloud-utils-master/external/manifold/src/main.cpp:4:
  /home/abelgomes/point-cloud-utils-master/external/manifold/3rd/Eigen/src/Core/functors/StlFunctors.h:87:28: warning: ‘template<class _Predicate> class std::unary_negate’ is deprecated [-Wdeprecated-declarations]
     87 | struct functor_traits<std::unary_negate<T> >
        |                            ^~~~~~~~~~~~
  In file included from /usr/include/c++/13/string:49,
                   from /usr/include/c++/13/bits/locale_classes.h:40,
                   from /usr/include/c++/13/bits/ios_base.h:41,
                   from /usr/include/c++/13/ios:44,
                   from /usr/include/c++/13/ostream:40,
                   from /usr/include/c++/13/iostream:41,
                   from /home/abelgomes/point-cloud-utils-master/external/manifold/src/Model_OBJ.h:4:
  /usr/include/c++/13/bits/stl_function.h:1024:33: note: declared here
   1024 |     class _GLIBCXX17_DEPRECATED unary_negate
        |                                 ^~~~~~~~~~~~
  /home/abelgomes/point-cloud-utils-master/external/manifold/3rd/Eigen/src/Core/functors/StlFunctors.h:91:28: warning: ‘template<class _Predicate> class std::binary_negate’ is deprecated [-Wdeprecated-declarations]
     91 | struct functor_traits<std::binary_negate<T> >
        |                            ^~~~~~~~~~~~~
  /usr/include/c++/13/bits/stl_function.h:1051:33: note: declared here
   1051 |     class _GLIBCXX17_DEPRECATED binary_negate
        |                                 ^~~~~~~~~~~~~
  In file included from /home/abelgomes/point-cloud-utils-master/external/manifold/3rd/Eigen/Core:405,
                   from /home/abelgomes/point-cloud-utils-master/external/manifold/3rd/igl/readOBJ.h:18,
                   from /home/abelgomes/point-cloud-utils-master/external/manifold/src/Model_OBJ.h:20,
                   from /home/abelgomes/point-cloud-utils-master/external/manifold/src/Model_OBJ.cpp:1:
  /home/abelgomes/point-cloud-utils-master/external/manifold/3rd/Eigen/src/Core/functors/StlFunctors.h:87:28: warning: ‘template<class _Predicate> class std::unary_negate’ is deprecated [-Wdeprecated-declarations]
     87 | struct functor_traits<std::unary_negate<T> >
        |                            ^~~~~~~~~~~~
  In file included from /usr/include/c++/13/string:49,
                   from /usr/include/c++/13/bits/locale_classes.h:40,
                   from /usr/include/c++/13/bits/ios_base.h:41,
                   from /usr/include/c++/13/ios:44,
                   from /usr/include/c++/13/ostream:40,
                   from /usr/include/c++/13/iostream:41,
                   from /home/abelgomes/point-cloud-utils-master/external/manifold/src/Model_OBJ.h:4:
  /usr/include/c++/13/bits/stl_function.h:1024:33: note: declared here
   1024 |     class _GLIBCXX17_DEPRECATED unary_negate
        |                                 ^~~~~~~~~~~~
  /home/abelgomes/point-cloud-utils-master/external/manifold/3rd/Eigen/src/Core/functors/StlFunctors.h:91:28: warning: ‘template<class _Predicate> class std::binary_negate’ is deprecated [-Wdeprecated-declarations]
     91 | struct functor_traits<std::binary_negate<T> >
        |                            ^~~~~~~~~~~~~
  /usr/include/c++/13/bits/stl_function.h:1051:33: note: declared here
   1051 |     class _GLIBCXX17_DEPRECATED binary_negate
        |                                 ^~~~~~~~~~~~~
  [  3%] Linking CXX static library libmanifold.a
  [  3%] Built target manifold
  gmake: *** [Makefile:166: all] Error 2
  Traceback (most recent call last):
    File "/usr/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/usr/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
      return _build_backend().build_wheel(wheel_directory, config_settings,
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 410, in build_wheel
      return self._build_with_temp_dir(
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 395, in _build_with_temp_dir
      self.run_setup()
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 311, in run_setup
      exec(code, locals())
    File "<string>", line 116, in <module>
    File "<string>", line 89, in main
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 103, in setup
      return distutils.core.setup(**attrs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 184, in setup
      return run_commands(dist)
             ^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 200, in run_commands
      dist.run_commands()
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
      self.run_command(cmd)
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 968, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/wheel/bdist_wheel.py", line 368, in run
      self.run_command("build")
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 968, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/_distutils/command/build.py", line 132, in run
      self.run_command(cmd_name)
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
      self.distribution.run_command(command)
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 968, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-tm3h_bp7/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "<string>", line 39, in run
    File "<string>", line 72, in build_extension
    File "/usr/lib64/python3.12/subprocess.py", line 413, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for point-cloud-utils
Failed to build point-cloud-utils
ERROR: Could not build wheels for point-cloud-utils, which is required to install pyproject.toml-based projects