BUG: Can't install 1.9.1 on arm32v7 Ubuntu Focal (py3.8) from source

Describe your issue.

We maintain a wheel repo for use with our docker images and we currently build scipy on arm32v7 for Ubuntu Focal and Jammy. Unfortunately 1.9.1 does not build on Ubuntu Focal (python 3.8). It builds fine on Ubuntu Jammy (python 3.10)

Here’s the dockerfile we use: https://github.com/linuxserver/wheelie/blob/main/Dockerfile.sci You can ignore the bits about qpdf, which is only needed when building pikepdf and gets skipped when only building scipy (same dockerfile is used for scipy, scikit-learn and pikepdf). distro, arch and packages to build get injected as build args in a jenkins pipeline

Here’s the arm32v7 build log on Ubuntu Focal (native hardware, rpi4): https://ci.linuxserver.io/blue/rest/organizations/jenkins/pipelines/Tools/pipelines/wheelieSCI/runs/64/nodes/24/steps/196/log/?start=0

Here’s the full build log that also lists the Jammy build: https://ci.linuxserver.io/blue/organizations/jenkins/Tools%2FwheelieSCI/detail/wheelieSCI/64/pipeline

Reproducing Code Example

  python3 -m venv /build-env && \
  . /build-env/bin/activate && \
  pip3 install -U pip setuptools wheel cython && \
  pip wheel --wheel-dir=/build -v ninja patchelf && \
  pip install /build/ninja-* /build/patchelf-* && \
  pip wheel --wheel-dir=/build -v scipy

Error message

  Copying files to wheel...
  [0/1224] scipy/__config__.py
  [1/1224] scipy/version.py
  [2/1224] scipy/_lib/_ccallback_c.cpython-38-arm-linux-gnueabihf.so
  Traceback (most recent call last):
    File "/build-env/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 156, in prepare_metadata_for_build_wheel
      hook = backend.prepare_metadata_for_build_wheel
  AttributeError: module 'mesonpy' has no attribute 'prepare_metadata_for_build_wheel'

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/build-env/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
      main()
    File "/build-env/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/build-env/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 160, in prepare_metadata_for_build_wheel
      whl_basename = backend.build_wheel(metadata_directory, config_settings)
    File "/tmp/pip-build-env-_kuqgyjz/overlay/lib/python3.8/site-packages/mesonpy/__init__.py", line 941, in build_wheel
      return project.wheel(out).name
    File "/tmp/pip-build-env-_kuqgyjz/overlay/lib/python3.8/site-packages/mesonpy/__init__.py", line 889, in wheel
      wheel = _WheelBuilder(self).build(self._install_plan, self._copy_files, self._build_dir)
    File "/tmp/pip-build-env-_kuqgyjz/overlay/lib/python3.8/site-packages/mesonpy/__init__.py", line 380, in build
      self._install_file(whl, counter, origin, destination)
    File "/tmp/pip-build-env-_kuqgyjz/overlay/lib/python3.8/site-packages/mesonpy/__init__.py", line 341, in _install_file
      if libdir_path not in elf.rpath:
    File "/tmp/pip-build-env-_kuqgyjz/overlay/lib/python3.8/site-packages/mesonpy/_elf.py", line 25, in rpath
      self._rpath = self._patchelf('--print-rpath').strip().split(';')
    File "/tmp/pip-build-env-_kuqgyjz/overlay/lib/python3.8/site-packages/mesonpy/_elf.py", line 20, in _patchelf
      return subprocess.check_output(['patchelf', *args, self._path]).decode()
    File "/usr/lib/python3.8/subprocess.py", line 415, in check_output
      return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
    File "/usr/lib/python3.8/subprocess.py", line 516, in run
      raise CalledProcessError(retcode, process.args,
  subprocess.CalledProcessError: Command '['patchelf', '--print-rpath', '/tmp/pip-wheel-vxwycymm/scipy_404354316b954b23970a8fe4d3f56ab8/.mesonpy-6rz_hsfb/build/mesonpy-wheel-libs/scipy/_lib/_ccallback_c.cpython-38-arm-linux-gnueabihf.so']' returned non-zero exit status 1.
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) 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.
  full command: /build-env/bin/python3 /build-env/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpsq2fne4h
  cwd: /tmp/pip-wheel-vxwycymm/scipy_404354316b954b23970a8fe4d3f56ab8
  Preparing metadata (pyproject.toml): finished with status 'error'
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.

SciPy/NumPy/Python version information

1.9.1

[rgommers]

Thanks @aptalca, that is helpful. The log shows two issues:

WARNING File matched Debian heuristic (scipy/odr/__odrpack.cpython-38-arm-linux-gnueabihf.so): /scipy/.mesonpy-jb8ktm8g/install/usr/lib/python3/dist-packages/scipy/odr/__odrpack.cpython-38-arm-linux-gnueabihf.so (/usr/lib/python3/dist-packages/scipy/odr/__odrpack.cpython-38-arm-linux-gnueabihf.so)

patchelf: /lib/arm-linux-gnueabihf/libc.so.6: version `GLIBC_2.33' not found (required by patchelf)

The patchelf warning is new, but we’re getting rid of the use of patchelf for SciPy completely in the new meson-python release that’s coming over the next few days.

The other one I’ve seen before. It should also be fixed in the new meson-python release. Once that is out, we should also get a SciPy 1.9.2 with accumulated fixes I think. Let me circle back to this once the meson-python release is available.

[rgommers]

Great, thanks for confirming @aptalca