Build error due to pybind11_mkdoc #121
Description
Hi,
I'm trying to build from source but am getting some errors.
My build instructions:
conda create --name mplib python=3.10
conda activate mplib
conda install -c conda-forge 'eigen=3.4.0' ompl fcl 'pinocchio=2.7.*' assimp orocos-kdl urdfdom pybind11 llvmdev clang hpp-fcl mkdocs -y
git submodule update --init --recursive
export CMAKE_BUILD_PARALLEL_LEVEL=10
python setup.py installA few questions:
- Are there build instructions anywhere?
- Is there a docker image anywhere?
- How can I fix this issue? This looks like a mkdoc issue but i'm not seeing an exact error
Thanks
Error:
(mplib) [ branch: main ] jstm ~/Projects/MPlib $ python setup.py install
/home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
!!
********************************************************************************
Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).
By 2026-Feb-18, you need to update your project and remove deprecated calls
or your builds will no longer be supported.
See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
********************************************************************************
!!
corresp(dist, value, root_dir)
/home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX license expression:
License :: OSI Approved :: MIT License
See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
********************************************************************************
!!
dist._finalize_license_expression()
/home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX license expression:
License :: OSI Approved :: MIT License
See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
********************************************************************************
!!
self._finalize_license_expression()
running install
/home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
This deprecation is overdue, please update your project and remove deprecated
calls to avoid build errors in the future.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running build
running build_py
copying mplib/__init__.py -> build/lib.linux-x86_64-cpython-310/mplib
copying mplib/planner.py -> build/lib.linux-x86_64-cpython-310/mplib
copying mplib/urdf_utils.py -> build/lib.linux-x86_64-cpython-310/mplib
copying mplib/collision_detection/fcl.py -> build/lib.linux-x86_64-cpython-310/mplib/collision_detection
copying mplib/collision_detection/__init__.py -> build/lib.linux-x86_64-cpython-310/mplib/collision_detection
copying mplib/examples/__init__.py -> build/lib.linux-x86_64-cpython-310/mplib/examples
copying mplib/examples/demo_setup.py -> build/lib.linux-x86_64-cpython-310/mplib/examples
copying mplib/examples/moving_robot.py -> build/lib.linux-x86_64-cpython-310/mplib/examples
copying mplib/examples/constrained_planning.py -> build/lib.linux-x86_64-cpython-310/mplib/examples
copying mplib/examples/collision_avoidance.py -> build/lib.linux-x86_64-cpython-310/mplib/examples
copying mplib/examples/two_stage_motion.py -> build/lib.linux-x86_64-cpython-310/mplib/examples
copying mplib/examples/demo.py -> build/lib.linux-x86_64-cpython-310/mplib/examples
copying mplib/examples/detect_collision.py -> build/lib.linux-x86_64-cpython-310/mplib/examples
copying mplib/sapien_utils/urdf_exporter.py -> build/lib.linux-x86_64-cpython-310/mplib/sapien_utils
copying mplib/sapien_utils/conversion.py -> build/lib.linux-x86_64-cpython-310/mplib/sapien_utils
copying mplib/sapien_utils/__init__.py -> build/lib.linux-x86_64-cpython-310/mplib/sapien_utils
copying mplib/sapien_utils/srdf_exporter.py -> build/lib.linux-x86_64-cpython-310/mplib/sapien_utils
copying mplib/kinematics/__init__.py -> build/lib.linux-x86_64-cpython-310/mplib/kinematics
copying mplib/kinematics/pinocchio.py -> build/lib.linux-x86_64-cpython-310/mplib/kinematics
copying mplib/kinematics/kdl.py -> build/lib.linux-x86_64-cpython-310/mplib/kinematics
copying mplib/planning/__init__.py -> build/lib.linux-x86_64-cpython-310/mplib/planning
copying mplib/planning/ompl.py -> build/lib.linux-x86_64-cpython-310/mplib/planning
running egg_info
writing mplib.egg-info/PKG-INFO
writing dependency_links to mplib.egg-info/dependency_links.txt
writing requirements to mplib.egg-info/requires.txt
writing top-level names to mplib.egg-info/top_level.txt
reading manifest file 'mplib.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'mplib.egg-info/SOURCES.txt'
/home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/setuptools/command/build_py.py:212: _Warning: Package 'mplib.pymp' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'mplib.pymp' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'mplib.pymp' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'mplib.pymp' to be distributed and are
already explicitly excluding 'mplib.pymp' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
/home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/setuptools/command/build_py.py:212: _Warning: Package 'mplib.pymp.collision_detection' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'mplib.pymp.collision_detection' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'mplib.pymp.collision_detection' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'mplib.pymp.collision_detection' to be distributed and are
already explicitly excluding 'mplib.pymp.collision_detection' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
/home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/setuptools/command/build_py.py:212: _Warning: Package 'mplib.pymp.kinematics' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'mplib.pymp.kinematics' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'mplib.pymp.kinematics' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'mplib.pymp.kinematics' to be distributed and are
already explicitly excluding 'mplib.pymp.kinematics' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
/home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/setuptools/command/build_py.py:212: _Warning: Package 'mplib.pymp.planning' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'mplib.pymp.planning' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'mplib.pymp.planning' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'mplib.pymp.planning' to be distributed and are
already explicitly excluding 'mplib.pymp.planning' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
copying mplib/py.typed -> build/lib.linux-x86_64-cpython-310/mplib
copying mplib/pymp/__init__.pyi -> build/lib.linux-x86_64-cpython-310/mplib/pymp
copying mplib/pymp/collision_detection/__init__.pyi -> build/lib.linux-x86_64-cpython-310/mplib/pymp/collision_detection
copying mplib/pymp/collision_detection/fcl.pyi -> build/lib.linux-x86_64-cpython-310/mplib/pymp/collision_detection
copying mplib/pymp/kinematics/__init__.pyi -> build/lib.linux-x86_64-cpython-310/mplib/pymp/kinematics
copying mplib/pymp/kinematics/kdl.pyi -> build/lib.linux-x86_64-cpython-310/mplib/pymp/kinematics
copying mplib/pymp/kinematics/pinocchio.pyi -> build/lib.linux-x86_64-cpython-310/mplib/pymp/kinematics
copying mplib/pymp/planning/__init__.pyi -> build/lib.linux-x86_64-cpython-310/mplib/pymp/planning
copying mplib/pymp/planning/ompl.pyi -> build/lib.linux-x86_64-cpython-310/mplib/pymp/planning
running build_ext
['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/jstm/Projects/MPlib/build/lib.linux-x86_64-cpython-310/mplib/', '-DPYTHON_EXECUTABLE=/home/jstm/miniconda3/envs/mplib/bin/python', '-DCMAKE_BUILD_TYPE=Release'] []
-- Found Boost: /home/jstm/miniconda3/envs/mplib/lib/cmake/Boost-1.82.0/BoostConfig.cmake (found version "1.82.0") found components: system filesystem
-- pinocchio not FOUND.
-- boost_filesystem FOUND. boost_filesystem at /home/jstm/miniconda3/envs/mplib/lib/libboost_filesystem.so
-- boost_serialization FOUND. boost_serialization at /home/jstm/miniconda3/envs/mplib/lib/libboost_serialization.so
-- boost_system FOUND. boost_system at /home/jstm/miniconda3/envs/mplib/lib/libboost_system.so
CMake Warning at /usr/share/cmake-3.16/Modules/FindBoost.cmake:1161 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1283 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1921 (_Boost_MISSING_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/pinocchio/pinocchioConfig.cmake:159 (find_dependency)
CMakeLists.txt:31 (find_package)
CMake Warning at /usr/share/cmake-3.16/Modules/FindBoost.cmake:1161 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1283 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1921 (_Boost_MISSING_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/pinocchio/pinocchioConfig.cmake:159 (find_dependency)
CMakeLists.txt:31 (find_package)
CMake Warning at /usr/share/cmake-3.16/Modules/FindBoost.cmake:1161 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1283 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1921 (_Boost_MISSING_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/pinocchio/pinocchioConfig.cmake:159 (find_dependency)
CMakeLists.txt:31 (find_package)
-- Found Boost: /home/jstm/miniconda3/envs/mplib/include (found version "1.82.0") found components: filesystem serialization system
-- eigenpy not FOUND.
-- For CMake < 3.18, Development.Module is not available. Falling back to Development
-- PythonLibraryDirs: /home/jstm/miniconda3/envs/mplib/lib
-- PythonLibVersionString: 3.10.19
-- Python site lib: lib/python3.10/site-packages
-- Python include dirs: /home/jstm/miniconda3/envs/mplib/include/python3.10
-- Checking for NumPy
-- NUMPY_INCLUDE_DIRS=/home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/numpy/core/include
-- NUMPY_VERSION=1.26.4
-- NumPy include dir: /home/jstm/miniconda3/envs/mplib/lib/python3.10/site-packages/numpy/core/include
CMake Warning at /usr/share/cmake-3.16/Modules/FindBoost.cmake:1161 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1283 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1921 (_Boost_MISSING_DEPENDENCIES)
/home/jstm/miniconda3/envs/mplib/lib/cmake/eigenpy/boost.cmake:144 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/eigenpy/eigenpyConfig.cmake:149 (SEARCH_FOR_BOOST_PYTHON)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/pinocchio/pinocchioConfig.cmake:160 (find_dependency)
CMakeLists.txt:31 (find_package)
CMake Warning at /usr/share/cmake-3.16/Modules/FindBoost.cmake:2020 (message):
No header defined for python310; skipping header check (note: header-only
libraries have no designated component)
Call Stack (most recent call first):
/home/jstm/miniconda3/envs/mplib/lib/cmake/eigenpy/boost.cmake:144 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/eigenpy/eigenpyConfig.cmake:149 (SEARCH_FOR_BOOST_PYTHON)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/pinocchio/pinocchioConfig.cmake:160 (find_dependency)
CMakeLists.txt:31 (find_package)
-- Found Boost: /home/jstm/miniconda3/envs/mplib/include (found version "1.82.0") found components: python310
-- Boost_PYTHON_LIBRARY: /home/jstm/miniconda3/envs/mplib/lib/libboost_python310.so
-- Default C++ standard: 201703
-- C++ standard sufficient: Minimal required 14, currently defined: 17
-- hpp-fcl not FOUND.
CMake Warning at /usr/share/cmake-3.16/Modules/FindBoost.cmake:1161 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1283 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1921 (_Boost_MISSING_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/hpp-fcl/hpp-fclConfig.cmake:154 (find_dependency)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/pinocchio/pinocchioConfig.cmake:161 (find_dependency)
CMakeLists.txt:31 (find_package)
CMake Warning at /usr/share/cmake-3.16/Modules/FindBoost.cmake:1161 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1283 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1921 (_Boost_MISSING_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/hpp-fcl/hpp-fclConfig.cmake:154 (find_dependency)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/pinocchio/pinocchioConfig.cmake:161 (find_dependency)
CMakeLists.txt:31 (find_package)
CMake Warning at /usr/share/cmake-3.16/Modules/FindBoost.cmake:1161 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1283 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/FindBoost.cmake:1921 (_Boost_MISSING_DEPENDENCIES)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/hpp-fcl/hpp-fclConfig.cmake:154 (find_dependency)
/usr/share/cmake-3.16/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/home/jstm/miniconda3/envs/mplib/lib/cmake/pinocchio/pinocchioConfig.cmake:161 (find_dependency)
CMakeLists.txt:31 (find_package)
-- Found Boost: /home/jstm/miniconda3/envs/mplib/include (found version "1.82.0") found components: chrono serialization filesystem
-- C++ standard sufficient: Minimal required 14, currently defined: 17
-- C++ standard sufficient: Minimal required 14, currently defined: 17
-- pybind11 v2.12.0 dev1
-- Configuring done
-- Generating done
-- Build files have been written to: /home/jstm/Projects/MPlib/build/temp.linux-x86_64-cpython-310/mplib.pymp
Traceback (most recent call last):
File "/home/jstm/Projects/MPlib/dev/mkdoc.py", line 59, in <module>
from clang import cindex
ModuleNotFoundError: No module named 'clang'
...
Traceback (most recent call last):
File "/home/jstm/Projects/MPlib/dev/mkdoc.py", line 59, in <module>
from clang import cindex
ModuleNotFoundError: No module named 'clang'
Traceback (most recent call last):
File "/home/jstm/Projects/MPlib/dev/mkdoc.py", line 59, in <module>
from clang import cindex
ModuleNotFoundError: No module named 'clang'
Caught error in /home/jstm/Projects/MPlib/dev/mkdoc.sh:51 ('wait $(jobs -rp)' exited with status 1)
Traceback (most recent call last, command might not be complete):
(0) /home/jstm/Projects/MPlib/dev/mkdoc.sh:51 'wait $(jobs -rp)'
make[2]: *** [CMakeFiles/pybind11_mkdoc.dir/build.make:78: CMakeFiles/pybind11_mkdoc] Error 1
make[1]: *** [CMakeFiles/Makefile2:157: CMakeFiles/pybind11_mkdoc.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 2%] Building CXX object CMakeFiles/mp.dir/src/collision_detection/fcl/collision_common.cpp.o
[ 5%] Building CXX object CMakeFiles/mp.dir/src/kinematics/pinocchio/pinocchio_model.cpp.o