Build error when installing with pip

[WanqingXia]

I am using PyCharm virtual env to install pin, I met the following build error. I have tried to install cmeel but it does not fix the problem. Does anyone know how to fix this?

Thanks in advance.

(venvnew) (base) iai-lab@iailab-System-Product-Name:~/Documents/megapose6d$ pip install pin
Collecting pin
  Using cached pin-2.7.0.tar.gz (61.8 MB)
  Installing build dependencies ... error
  error: subprocess-exited-with-error
  
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [62 lines of output]
      Collecting cmeel-boost~=1.83.0
        Using cached cmeel_boost-1.83.0.tar.gz (4.0 kB)
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'error'
        error: subprocess-exited-with-error
      
        × Preparing metadata (pyproject.toml) did not run successfully.
        │ exit code: 1
        ╰─> [39 lines of output]
            -- The C compiler identification is GNU 7.5.0
            -- The CXX compiler identification is GNU 7.5.0
            -- 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 Error at /tmp/pip-build-env-s9j092i6/overlay/lib/python3.9/site-packages/cmake/data/share/cmake-3.29/Modules/FindPython/Support.cmake:719 (file):
              file STRINGS file
              "/home/iai-lab/Downloads/Python-3.9.19/Include/pyconfig.h" cannot be read.
            Call Stack (most recent call first):
              /tmp/pip-build-env-s9j092i6/overlay/lib/python3.9/site-packages/cmake/data/share/cmake-3.29/Modules/FindPython/Support.cmake:3569 (_python_get_version)
              /tmp/pip-build-env-s9j092i6/overlay/lib/python3.9/site-packages/cmake/data/share/cmake-3.29/Modules/FindPython3.cmake:545 (include)
              CMakeLists.txt:11 (find_package)
      
      
            -- Found Python3: /home/iai-lab/Documents/SiameseViT/venvnew/bin/python (found version "3.9.19") found components: Interpreter Development.Module
            -- CONFIGURE_COMMAND: ./bootstrap.sh;--prefix=/tmp/cmeel-6rb9gsy2/whl/cmeel.prefix
            -- BUILD_COMMAND: ./b2;hardcode-dll-paths=true;dll-path='$ORIGIN';link=shared;python=3.9
            -- Configuring incomplete, errors occurred!
            Traceback (most recent call last):
              File "/home/iai-lab/Documents/SiameseViT/venvnew/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
                main()
              File "/home/iai-lab/Documents/SiameseViT/venvnew/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
                json_out['return_val'] = hook(**hook_input['kwargs'])
              File "/home/iai-lab/Documents/SiameseViT/venvnew/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
                whl_basename = backend.build_wheel(metadata_directory, config_settings)
              File "/tmp/pip-build-env-s9j092i6/overlay/lib/python3.9/site-packages/cmeel/build.py", line 26, in build_wheel
                return build_impl(wheel_directory, editable=False)
              File "/tmp/pip-build-env-s9j092i6/overlay/lib/python3.9/site-packages/cmeel/impl.py", line 100, in build_impl
                check_call(configure_cmd, env=configure_env)
              File "/home/iai-lab/Downloads/Python-3.9.19/Lib/subprocess.py", line 373, in check_call
                raise CalledProcessError(retcode, cmd)
            subprocess.CalledProcessError: Command '['cmake', '-S', '.', '-B', '/tmp/cmeel-6rb9gsy2/bld', '-DBoost_NO_WARN_NEW_VERSIONS=ON', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_INSTALL_LIBDIR=lib', '-DCMAKE_INSTALL_PREFIX=/tmp/cmeel-6rb9gsy2/whl/cmeel.prefix', '-DPYTHON_SITELIB=lib/python3.9/site-packages', '-DPython3_EXECUTABLE=/home/iai-lab/Documents/SiameseViT/venvnew/bin/python', '-DCMAKE_APPLE_SILICON_PROCESSOR=arm64', '-DCMEEL_JOBS=4', '-DBUILD_TESTING=OFF']' returned non-zero exit status 1.
            [end of output]
      
        note: This error originates from a subprocess, and is likely not a problem with pip.
      error: metadata-generation-failed
      
      × Encountered error while generating package metadata.
      ╰─> See above for output.
      
      note: This is an issue with the package mentioned above, not pip.
      hint: See above for details.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

System

• OS: Ubuntu 20.04
• Python version: 3.9

[jcarpent]

One quick alternative is to rely on conda and use conda install -c conda-forge pinocchio.

[joao-pm-santos96]

Hi @jcarpent ! If I want to help fix this issue, where should I start?

[stephane-caron]

Do you have the exact same error, though? If I had to guess, the main error in the log above is "/home/iai-lab/Downloads/Python-3.9.19/Include/pyconfig.h" cannot be read. which looks like specific to the installation of the system the error ran on.

If you have the exact same error, you should start by giving more details on how you got there (how was Python installed? how was the virtual env created? full list of packages that were installed from PyPI, etc.) You can also try to break down the package installation error to the first dependency that doesn't work.

If after reading your logs carefully you realize you have a different error: same process but in a different post 😉

[stephane-caron]

@WanqingXia: these two points are also feedback to your original issue. From reading your logs, it seems the first dependency that doesn't work is "cmeel-boost": you can then try to pip install cmeel-boost directly, and if it doesn't work report all details in an issue of the cmeel-boost issue tracker. That way the underlying problem to solve will be reduced.

[joao-pm-santos96]

My apologies, I missed understood the original issue. I didn't realize that it was a local installation and assumed that @WanqingXia was talking about some GitHub Action that should publish Pinocchio to pypi but was falling. Short answer, I do not have this issue. Once again, my apologies...

[nim65s]

you can then try to pip install cmeel-boost directly

This is not the right time: I am currently upgrading cmeel-boost. It will take some time while cmeel boost 1.84 is available, and eigenpy and pinocchio binaries are not ready for boost 1.84.

@WanqingXia : we have working binaries, so I'd first like to know why you are building from source. Can you provide your python version, pip version, OS and architecture ?

[nim65s]

Ok, I saw 20.04 (I assume x86_64) and py 3.9. How did you install python 3.9 on ubuntu 20.04 ?

[WanqingXia]

Ok, I saw 20.04 (I assume x86_64) and py 3.9. How did you install python 3.9 on ubuntu 20.04 ?

Thank you for still tracking this issue. I downloaded python 3.9 from the official website Gzipped source tarball. After installing it, I used it as the interpreter in my PyCharm venv.

[nim65s]

Ok, I tried to reproduce your issue in a Dockerfile, and it is working for me. Is there anything you did differently ?

FROM ubuntu:20.04

ADD https://www.python.org/ftp/python/3.9.16/Python-3.9.16.tgz /

# https://devguide.python.org/getting-started/setup-building/#build-dependencies
RUN echo 'deb-src http://archive.ubuntu.com/ubuntu/ focal main' >> /etc/apt/sources.list
RUN --mount=type=cache,sharing=locked,target=/var/cache/apt \
    --mount=type=cache,sharing=locked,target=/var/lib/apt \
    apt-get update -y && DEBIAN_FRONTEND=noninteractive apt-get install -qqy --no-install-recommends \
    build-essential gdb lcov pkg-config \
    libbz2-dev libffi-dev libgdbm-dev libgdbm-compat-dev liblzma-dev \
    libncurses5-dev libreadline6-dev libsqlite3-dev libssl-dev \
    lzma lzma-dev tk-dev uuid-dev zlib1g-dev libmpdec-dev

RUN tar xf /Python-3.9.16.tgz
WORKDIR /Python-3.9.16
RUN ./configure \
 && make \
 && make install

RUN python3 -m venv venv \
 && . venv/bin/activate \
 && pip install pin

To me, this correctly lead to:

(venv) root@bd359d543fb1:/Python-3.9.16# python -V
Python 3.9.16
(venv) root@bd359d543fb1:/Python-3.9.16# python -c "import pinocchio as pin; print(pin.__version__)"
2.7.0

[WanqingXia]

I tried to create a new venv with python 3.9 and install pip, the problem still exists. Here is the full output

(venv) iai-lab@iailab-System-Product-Name:~/Downloads$ pip install pin
Collecting pin
  Using cached pin-2.7.0.tar.gz (61.8 MB)
  Installing build dependencies ... error
  error: subprocess-exited-with-error
  
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [160 lines of output]
      Collecting cmeel-boost~=1.83.0
        Using cached cmeel_boost-1.83.0-0-cp39-cp39-manylinux_2_27_x86_64.whl
      Collecting cmeel-urdfdom[build]<4,>=3.1.1.1
        Using cached cmeel_urdfdom-3.1.1.1.tar.gz (292 kB)
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'done'
      Collecting cmeel[build]
        Using cached cmeel-0.53.3-py3-none-any.whl (20 kB)
      Collecting hpp-fcl[build]<4,>=2.3.4
        Using cached hpp_fcl-2.4.4.tar.gz (3.2 MB)
        Installing build dependencies: started
        Installing build dependencies: still running...
        Installing build dependencies: still running...
        Installing build dependencies: finished with status 'error'
        error: subprocess-exited-with-error
      
        × pip subprocess to install build dependencies did not run successfully.
        │ exit code: 1
        ╰─> [124 lines of output]
            Collecting cmeel-assimp<6,>=5.3.1
              Using cached cmeel_assimp-5.3.1.tar.gz (52.6 MB)
              Installing build dependencies: started
              Installing build dependencies: finished with status 'done'
              Getting requirements to build wheel: started
              Getting requirements to build wheel: finished with status 'done'
              Preparing metadata (pyproject.toml): started
              Preparing metadata (pyproject.toml): still running...
              Preparing metadata (pyproject.toml): still running...
              Preparing metadata (pyproject.toml): finished with status 'done'
            Collecting cmeel-boost~=1.83.0
              Using cached cmeel_boost-1.83.0-0-cp39-cp39-manylinux_2_27_x86_64.whl
            Collecting cmeel-octomap<2,>=1.9.8.2
              Using cached cmeel_octomap-1.9.8.2.tar.gz (1.7 MB)
              Installing build dependencies: started
              Installing build dependencies: finished with status 'done'
              Getting requirements to build wheel: started
              Getting requirements to build wheel: finished with status 'done'
              Preparing metadata (pyproject.toml): started
              Preparing metadata (pyproject.toml): finished with status 'done'
            Collecting cmeel-qhull<8.0.3,>=8.0.2.1
              Using cached cmeel_qhull-8.0.2.1.tar.gz (1.3 MB)
              Installing build dependencies: started
              Installing build dependencies: finished with status 'done'
              Getting requirements to build wheel: started
              Getting requirements to build wheel: finished with status 'done'
              Preparing metadata (pyproject.toml): started
              Preparing metadata (pyproject.toml): finished with status 'done'
            Collecting cmeel[build]
              Using cached cmeel-0.53.3-py3-none-any.whl (20 kB)
            Collecting eigenpy[build]<4,>=3.1
              Using cached eigenpy-3.5.1.tar.gz (1.0 MB)
              Installing build dependencies: started
              Installing build dependencies: finished with status 'done'
              Getting requirements to build wheel: started
              Getting requirements to build wheel: finished with status 'done'
              Preparing metadata (pyproject.toml): started
              Preparing metadata (pyproject.toml): finished with status 'error'
              error: subprocess-exited-with-error
      
              × Preparing metadata (pyproject.toml) did not run successfully.
              │ exit code: 1
              ╰─> [68 lines of output]
                  -- JRL cmakemodules found in 'cmake/' git submodule
                  -- Configuring "eigenpy" (http://github.com/stack-of-tasks/eigenpy)
                  -- Package version (ROS package.xml): 3.5.1
                  -- The CXX compiler identification is GNU 7.5.0
                  -- 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
                  -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
                  -- Performing Test res_-pedantic
                  -- Performing Test res_-pedantic - Success
                  -- Performing Test res_-Wno-long-long
                  -- Performing Test res_-Wno-long-long - Success
                  -- Performing Test res_-Wall
                  -- Performing Test res_-Wall - Success
                  -- Performing Test res_-Wextra
                  -- Performing Test res_-Wextra - Success
                  -- Performing Test res_-Wcast-align
                  -- Performing Test res_-Wcast-align - Success
                  -- Performing Test res_-Wcast-qual
                  -- Performing Test res_-Wcast-qual - Success
                  -- Performing Test res_-Wformat
                  -- Performing Test res_-Wformat - Success
                  -- Performing Test res_-Wwrite-strings
                  -- Performing Test res_-Wwrite-strings - Success
                  -- Performing Test res_-Wconversion
                  -- Performing Test res_-Wconversion - Success
                  -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
                  -- Failed to find Doxygen, documentation will not be generated.
                  -- Default C++ standard: 201402
                  -- Minimal C++ standard upgraded to 11
                  -- C++ standard sufficient: Minimal required 11, currently defined: 14
                  -- CMAKE_CXX_STANDARD was not set: automatically set to currently defined standard 14
                  -- Found Python3: /home/iai-lab/Downloads/venv/bin/python3.9 (found version "3.9.19") found components: Interpreter Development.Module NumPy
                  -- PythonLibraryDirs:
                  -- PythonLibVersionString: 3.9.19
                  -- Python site lib: lib/python3.9/site-packages
                  -- Python include dirs: /usr/local/include/python3.9
                  -- Checking for NumPy
                  --   NUMPY_INCLUDE_DIRS=/tmp/pip-build-env-kzrkho3q/overlay/lib/python3.9/site-packages/numpy/core/include
                  --   NUMPY_VERSION=1.26.4
                  -- NumPy include dir: /tmp/pip-build-env-kzrkho3q/overlay/lib/python3.9/site-packages/numpy/core/include
                  -- Found Boost: /tmp/pip-build-env-kzrkho3q/overlay/lib/python3.9/site-packages/cmeel.prefix/include (found version "1.83.0")
                  -- Found Boost: /tmp/pip-build-env-kzrkho3q/overlay/lib/python3.9/site-packages/cmeel.prefix/include (found version "1.83.0") found components: python39
                  -- Boost_PYTHON_LIBRARY: /tmp/pip-build-env-kzrkho3q/overlay/lib/python3.9/site-packages/cmeel.prefix/lib/libboost_python39.so
                  -- Checking for SciPy
                  CMake Error at cmake/python.cmake:544 (message):
                    Failed to detect scipy
                  Call Stack (most recent call first):
                    unittest/CMakeLists.txt:34 (find_scipy)
      
      
                  -- Configuring incomplete, errors occurred!
                  Traceback (most recent call last):
                    File "/home/iai-lab/Downloads/venv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
                      main()
                    File "/home/iai-lab/Downloads/venv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
                      json_out['return_val'] = hook(**hook_input['kwargs'])
                    File "/home/iai-lab/Downloads/venv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
                      whl_basename = backend.build_wheel(metadata_directory, config_settings)
                    File "/tmp/pip-build-env-kzrkho3q/overlay/lib/python3.9/site-packages/cmeel/build.py", line 26, in build_wheel
                      return build_impl(wheel_directory, editable=False)
                    File "/tmp/pip-build-env-kzrkho3q/overlay/lib/python3.9/site-packages/cmeel/impl.py", line 100, in build_impl
                      check_call(configure_cmd, env=configure_env)
                    File "/usr/local/lib/python3.9/subprocess.py", line 373, in check_call
                      raise CalledProcessError(retcode, cmd)
                  subprocess.CalledProcessError: Command '['cmake', '-S', '.', '-B', '/tmp/cmeel-03_xxyse/bld', '-DBoost_NO_WARN_NEW_VERSIONS=ON', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_INSTALL_LIBDIR=lib', '-DCMAKE_INSTALL_PREFIX=/tmp/cmeel-03_xxyse/whl/cmeel.prefix', '-DPYTHON_SITELIB=lib/python3.9/site-packages', '-DPython3_EXECUTABLE=/home/iai-lab/Downloads/venv/bin/python3.9', '-DCMAKE_APPLE_SILICON_PROCESSOR=arm64', '-DCMEEL_JOBS=4', '-DBUILD_TESTING=OFF']' returned non-zero exit status 1.
                  [end of output]
      
              note: This error originates from a subprocess, and is likely not a problem with pip.
            error: metadata-generation-failed
      
            × Encountered error while generating package metadata.
            ╰─> See above for output.
      
            note: This is an issue with the package mentioned above, not pip.
            hint: See above for details.
      
            [notice] A new release of pip is available: 23.0.1 -> 24.0
            [notice] To update, run: pip install --upgrade pip
            [end of output]
      
        note: This error originates from a subprocess, and is likely not a problem with pip.
      error: subprocess-exited-with-error
      
      × pip subprocess to install build dependencies did not run successfully.
      │ exit code: 1
      ╰─> See above for output.
      
      note: This error originates from a subprocess, and is likely not a problem with pip.
      
      [notice] A new release of pip is available: 23.0.1 -> 24.0
      [notice] To update, run: pip install --upgrade pip
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[notice] A new release of pip is available: 23.0.1 -> 24.0
[notice] To update, run: pip install --upgrade pip

[WanqingXia]

I also tried to manually install cmeel-boost first before installing pin

But the output suggest the same error

(venv) iai-lab@iailab-System-Product-Name:~/Downloads$ pip install pin
Collecting pin
  Using cached pin-2.7.0.tar.gz (61.8 MB)
  Installing build dependencies ... error
  error: subprocess-exited-with-error
  
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [75 lines of output]
      Collecting cmeel-boost~=1.83.0
        Using cached cmeel_boost-1.83.0-0-cp39-cp39-manylinux_2_27_x86_64.whl
      Collecting cmeel-urdfdom[build]<4,>=3.1.1.1
        Using cached cmeel_urdfdom-3.1.1.1.tar.gz (292 kB)
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'error'
        error: subprocess-exited-with-error
      
        × Preparing metadata (pyproject.toml) did not run successfully.
        │ exit code: 1
        ╰─> [47 lines of output]
            -- The CXX compiler identification is GNU 7.5.0
            -- The C compiler identification is GNU 7.5.0
            -- 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
            -- 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
            -- urdfdom version 3.0.2
            -- Performing Test HAS_VISIBILITY
            -- Performing Test HAS_VISIBILITY - Success
            CMake Error at CMakeLists.txt:48 (find_package):
              By not providing "Findtinyxml.cmake" in CMAKE_MODULE_PATH this project has
              asked CMake to find a package configuration file provided by "tinyxml", but
              CMake did not find one.
      
              Could not find a package configuration file provided by "tinyxml" with any
              of the following names:
      
                tinyxmlConfig.cmake
                tinyxml-config.cmake
      
              Add the installation prefix of "tinyxml" to CMAKE_PREFIX_PATH or set
              "tinyxml_DIR" to a directory containing one of the above files.  If
              "tinyxml" provides a separate development package or SDK, be sure it has
              been installed.
      
      
            -- Configuring incomplete, errors occurred!
            Traceback (most recent call last):
              File "/home/iai-lab/Downloads/venv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
                main()
              File "/home/iai-lab/Downloads/venv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
                json_out['return_val'] = hook(**hook_input['kwargs'])
              File "/home/iai-lab/Downloads/venv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
                whl_basename = backend.build_wheel(metadata_directory, config_settings)
              File "/tmp/pip-build-env-xjo43wfa/overlay/lib/python3.9/site-packages/cmeel/build.py", line 26, in build_wheel
                return build_impl(wheel_directory, editable=False)
              File "/tmp/pip-build-env-xjo43wfa/overlay/lib/python3.9/site-packages/cmeel/impl.py", line 100, in build_impl
                check_call(configure_cmd, env=configure_env)
              File "/usr/local/lib/python3.9/subprocess.py", line 373, in check_call
                raise CalledProcessError(retcode, cmd)
            subprocess.CalledProcessError: Command '['cmake', '-S', 'urdfdom', '-B', '/tmp/cmeel-e_jmovi6/bld', '-DBoost_NO_WARN_NEW_VERSIONS=ON', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_INSTALL_LIBDIR=lib', '-DCMAKE_INSTALL_PREFIX=/tmp/cmeel-e_jmovi6/whl/cmeel.prefix', '-DPYTHON_SITELIB=lib/python3.9/site-packages', '-DPython3_EXECUTABLE=/home/iai-lab/Downloads/venv/bin/python3.9', '-DCMAKE_APPLE_SILICON_PROCESSOR=arm64', '-DCMEEL_JOBS=4']' returned non-zero exit status 1.
            [end of output]
      
        note: This error originates from a subprocess, and is likely not a problem with pip.
      error: metadata-generation-failed
      
      × Encountered error while generating package metadata.
      ╰─> See above for output.
      
      note: This is an issue with the package mentioned above, not pip.
      hint: See above for details.
      
      [notice] A new release of pip is available: 23.0.1 -> 24.0
      [notice] To update, run: pip install --upgrade pip
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[notice] A new release of pip is available: 23.0.1 -> 24.0
[notice] To update, run: pip install --upgrade pip

[nim65s]

• You use a python3.9 activate venv command, which does not exist, so this is certainly not doing what you expect: https://docs.python.org/3/library/venv.html#how-venvs-work
• You say you "install pip", but your logs plainly display your pip is not up to date: A new release of pip is available: 23.0.1 -> 24.0, so don't know what you actually did, but that was wrong. And it is not necessary.

Please just try again correctly. There are 3 commands to run, and I already provided those:

python3.9 -m venv new-venv
source new-venv/bin/activate
pip install pin

[WanqingXia]

iai-lab@iailab-System-Product-Name:/Downloads$ python3.9 -m venv new-venv
iai-lab@iailab-System-Product-Name:/Downloads$ source new-venv/bin/activate
(new-venv) iai-lab@iailab-System-Product-Name:~/Downloads$ pip install pin

Collecting pin
  Using cached pin-2.7.0.tar.gz (61.8 MB)
  Installing build dependencies ... error
  error: subprocess-exited-with-error
  
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [160 lines of output]
      Collecting cmeel-boost~=1.83.0
        Using cached cmeel_boost-1.83.0-0-cp39-cp39-manylinux_2_27_x86_64.whl
      Collecting cmeel-urdfdom[build]<4,>=3.1.1.1
        Using cached cmeel_urdfdom-3.1.1.1.tar.gz (292 kB)
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'done'
      Collecting cmeel[build]
        Using cached cmeel-0.53.3-py3-none-any.whl (20 kB)
      Collecting hpp-fcl[build]<4,>=2.3.4
        Using cached hpp_fcl-2.4.4.tar.gz (3.2 MB)
        Installing build dependencies: started
        Installing build dependencies: still running...
        Installing build dependencies: still running...
        Installing build dependencies: finished with status 'error'
        error: subprocess-exited-with-error
      
        × pip subprocess to install build dependencies did not run successfully.
        │ exit code: 1
        ╰─> [124 lines of output]
            Collecting cmeel-assimp<6,>=5.3.1
              Using cached cmeel_assimp-5.3.1.tar.gz (52.6 MB)
              Installing build dependencies: started
              Installing build dependencies: finished with status 'done'
              Getting requirements to build wheel: started
              Getting requirements to build wheel: finished with status 'done'
              Preparing metadata (pyproject.toml): started
              Preparing metadata (pyproject.toml): still running...
              Preparing metadata (pyproject.toml): still running...
              Preparing metadata (pyproject.toml): finished with status 'done'
            Collecting cmeel-boost~=1.83.0
              Using cached cmeel_boost-1.83.0-0-cp39-cp39-manylinux_2_27_x86_64.whl
            Collecting cmeel-octomap<2,>=1.9.8.2
              Using cached cmeel_octomap-1.9.8.2.tar.gz (1.7 MB)
              Installing build dependencies: started
              Installing build dependencies: finished with status 'done'
              Getting requirements to build wheel: started
              Getting requirements to build wheel: finished with status 'done'
              Preparing metadata (pyproject.toml): started
              Preparing metadata (pyproject.toml): finished with status 'done'
            Collecting cmeel-qhull<8.0.3,>=8.0.2.1
              Using cached cmeel_qhull-8.0.2.1.tar.gz (1.3 MB)
              Installing build dependencies: started
              Installing build dependencies: finished with status 'done'
              Getting requirements to build wheel: started
              Getting requirements to build wheel: finished with status 'done'
              Preparing metadata (pyproject.toml): started
              Preparing metadata (pyproject.toml): finished with status 'done'
            Collecting cmeel[build]
              Using cached cmeel-0.53.3-py3-none-any.whl (20 kB)
            Collecting eigenpy[build]<4,>=3.1
              Using cached eigenpy-3.5.1.tar.gz (1.0 MB)
              Installing build dependencies: started
              Installing build dependencies: finished with status 'done'
              Getting requirements to build wheel: started
              Getting requirements to build wheel: finished with status 'done'
              Preparing metadata (pyproject.toml): started
              Preparing metadata (pyproject.toml): finished with status 'error'
              error: subprocess-exited-with-error
      
              × Preparing metadata (pyproject.toml) did not run successfully.
              │ exit code: 1
              ╰─> [68 lines of output]
                  -- JRL cmakemodules found in 'cmake/' git submodule
                  -- Configuring "eigenpy" (http://github.com/stack-of-tasks/eigenpy)
                  -- Package version (ROS package.xml): 3.5.1
                  -- The CXX compiler identification is GNU 7.5.0
                  -- 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
                  -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
                  -- Performing Test res_-pedantic
                  -- Performing Test res_-pedantic - Success
                  -- Performing Test res_-Wno-long-long
                  -- Performing Test res_-Wno-long-long - Success
                  -- Performing Test res_-Wall
                  -- Performing Test res_-Wall - Success
                  -- Performing Test res_-Wextra
                  -- Performing Test res_-Wextra - Success
                  -- Performing Test res_-Wcast-align
                  -- Performing Test res_-Wcast-align - Success
                  -- Performing Test res_-Wcast-qual
                  -- Performing Test res_-Wcast-qual - Success
                  -- Performing Test res_-Wformat
                  -- Performing Test res_-Wformat - Success
                  -- Performing Test res_-Wwrite-strings
                  -- Performing Test res_-Wwrite-strings - Success
                  -- Performing Test res_-Wconversion
                  -- Performing Test res_-Wconversion - Success
                  -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
                  -- Failed to find Doxygen, documentation will not be generated.
                  -- Default C++ standard: 201402
                  -- Minimal C++ standard upgraded to 11
                  -- C++ standard sufficient: Minimal required 11, currently defined: 14
                  -- CMAKE_CXX_STANDARD was not set: automatically set to currently defined standard 14
                  -- Found Python3: /home/iai-lab/Downloads/new-venv/bin/python3.9 (found version "3.9.19") found components: Interpreter Development.Module NumPy
                  -- PythonLibraryDirs:
                  -- PythonLibVersionString: 3.9.19
                  -- Python site lib: lib/python3.9/site-packages
                  -- Python include dirs: /usr/local/include/python3.9
                  -- Checking for NumPy
                  --   NUMPY_INCLUDE_DIRS=/tmp/pip-build-env-1k5kgv7s/overlay/lib/python3.9/site-packages/numpy/core/include
                  --   NUMPY_VERSION=1.26.4
                  -- NumPy include dir: /tmp/pip-build-env-1k5kgv7s/overlay/lib/python3.9/site-packages/numpy/core/include
                  -- Found Boost: /tmp/pip-build-env-1k5kgv7s/overlay/lib/python3.9/site-packages/cmeel.prefix/include (found version "1.83.0")
                  -- Found Boost: /tmp/pip-build-env-1k5kgv7s/overlay/lib/python3.9/site-packages/cmeel.prefix/include (found version "1.83.0") found components: python39
                  -- Boost_PYTHON_LIBRARY: /tmp/pip-build-env-1k5kgv7s/overlay/lib/python3.9/site-packages/cmeel.prefix/lib/libboost_python39.so
                  -- Checking for SciPy
                  CMake Error at cmake/python.cmake:544 (message):
                    Failed to detect scipy
                  Call Stack (most recent call first):
                    unittest/CMakeLists.txt:34 (find_scipy)
      
      
                  -- Configuring incomplete, errors occurred!
                  Traceback (most recent call last):
                    File "/home/iai-lab/Downloads/new-venv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
                      main()
                    File "/home/iai-lab/Downloads/new-venv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
                      json_out['return_val'] = hook(**hook_input['kwargs'])
                    File "/home/iai-lab/Downloads/new-venv/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
                      whl_basename = backend.build_wheel(metadata_directory, config_settings)
                    File "/tmp/pip-build-env-1k5kgv7s/overlay/lib/python3.9/site-packages/cmeel/build.py", line 26, in build_wheel
                      return build_impl(wheel_directory, editable=False)
                    File "/tmp/pip-build-env-1k5kgv7s/overlay/lib/python3.9/site-packages/cmeel/impl.py", line 100, in build_impl
                      check_call(configure_cmd, env=configure_env)
                    File "/usr/local/lib/python3.9/subprocess.py", line 373, in check_call
                      raise CalledProcessError(retcode, cmd)
                  subprocess.CalledProcessError: Command '['cmake', '-S', '.', '-B', '/tmp/cmeel-2iijs0_6/bld', '-DBoost_NO_WARN_NEW_VERSIONS=ON', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_INSTALL_LIBDIR=lib', '-DCMAKE_INSTALL_PREFIX=/tmp/cmeel-2iijs0_6/whl/cmeel.prefix', '-DPYTHON_SITELIB=lib/python3.9/site-packages', '-DPython3_EXECUTABLE=/home/iai-lab/Downloads/new-venv/bin/python3.9', '-DCMAKE_APPLE_SILICON_PROCESSOR=arm64', '-DCMEEL_JOBS=4', '-DBUILD_TESTING=OFF']' returned non-zero exit status 1.
                  [end of output]
      
              note: This error originates from a subprocess, and is likely not a problem with pip.
            error: metadata-generation-failed
      
            × Encountered error while generating package metadata.
            ╰─> See above for output.
      
            note: This is an issue with the package mentioned above, not pip.
            hint: See above for details.
      
            [notice] A new release of pip is available: 23.0.1 -> 24.0
            [notice] To update, run: pip install --upgrade pip
            [end of output]
      
        note: This error originates from a subprocess, and is likely not a problem with pip.
      error: subprocess-exited-with-error
      
      × pip subprocess to install build dependencies did not run successfully.
      │ exit code: 1
      ╰─> See above for output.
      
      note: This error originates from a subprocess, and is likely not a problem with pip.
      
      [notice] A new release of pip is available: 23.0.1 -> 24.0
      [notice] To update, run: pip install --upgrade pip
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[notice] A new release of pip is available: 23.0.1 -> 24.0
[notice] To update, run: pip install --upgrade pip

(new-venv) iai-lab@iailab-System-Product-Name:~/Downloads$

[nim65s]

Thanks. I don't understand why it can download some binaries but not others.

Please show me the output of this in the venv:

pip install packaging
python -c "from packaging.tags import sys_tags; print(next(sys_tags()))"

[WanqingXia]

Here is the output

iai-lab@iailab-System-Product-Name:~/Downloads$ source new-venv/bin/activate
(new-venv) iai-lab@iailab-System-Product-Name:~/Downloads$ pip install packagingCollecting packaging
  Using cached packaging-24.0-py3-none-any.whl (53 kB)
Installing collected packages: packaging
Successfully installed packaging-24.0

[notice] A new release of pip is available: 23.0.1 -> 24.0
[notice] To update, run: pip install --upgrade pip
(new-venv) iai-lab@iailab-System-Product-Name:~/Downloads$ python -c "from packaging.tags import sys_tags; print(next(sys_tags()))"
cp39-cp39-manylinux_2_27_x86_64

[stephane-caron]

Just chiming in that we encounter the same error when trying to install Pinocchio from PyPI in macos-latest GitHub runner images (online log, raw_log.txt):

My quick guess is that the relevant part is:

                     -- Checking for SciPy
                    CMake Error at cmake/python.cmake:544 (message):
                      Failed to detect scipy