0.18.0.0 seems to cause misaligned sections

[mathstuf]

Our CI started failing today using the manylinux2014 image. Given the symptom and the dist-info diff of a single installation (A/D seems to be backwards from what I'd expect):

% podman diff 879520bd4b55f4db71fb325219fe390c487f3d5409c4f89ea4201bbc1d18dd5b 4901c60f84c46a321c15d5283ed541efcbcf8c566bfc0cb52171af4cfa800d11 | grep dist-info$ | grep 3.10
C /opt/_internal/cpython-3.10.11/lib/python3.10/site-packages/tomli-2.0.1.dist-info
C /opt/_internal/cpython-3.10.11/lib/python3.10/site-packages/pyproject_hooks-1.0.0.dist-info
C /opt/_internal/cpython-3.10.11/lib/python3.10/site-packages/build-0.10.0.dist-info
C /opt/_internal/cpython-3.10.11/lib/python3.10/site-packages/packaging-23.1.dist-info
A /opt/_internal/cpython-3.10.11/lib/python3.10/site-packages/pip-23.1.dist-info
C /opt/_internal/cpython-3.10.11/lib/python3.10/site-packages/wheel-0.40.0.dist-info
A /opt/_internal/cpython-3.10.11/lib/python3.10/site-packages/setuptools-67.6.1.dist-info
D /opt/_internal/cpython-3.10.11/lib/python3.10/site-packages/setuptools-67.7.1.dist-info
D /opt/_internal/cpython-3.10.11/lib/python3.10/site-packages/pip-23.1.1.dist-info
C /opt/_internal/tools/lib/python3.10/site-packages/build-0.10.0.dist-info
C /opt/_internal/tools/lib/python3.10/site-packages/pyproject_hooks-1.0.0.dist-info
A /opt/_internal/tools/lib/python3.10/site-packages/setuptools-67.6.1.dist-info
A /opt/_internal/tools/lib/python3.10/site-packages/pip-23.1.dist-info
C /opt/_internal/tools/lib/python3.10/site-packages/pipx-1.2.0.dist-info
C /opt/_internal/tools/lib/python3.10/site-packages/userpath-1.8.0.dist-info
A /opt/_internal/tools/lib/python3.10/site-packages/argcomplete-3.0.5.dist-info
C /opt/_internal/tools/lib/python3.10/site-packages/certifi-2022.12.7.dist-info
C /opt/_internal/tools/lib/python3.10/site-packages/click-8.1.3.dist-info
C /opt/_internal/tools/lib/python3.10/site-packages/packaging-23.1.dist-info
C /opt/_internal/tools/lib/python3.10/site-packages/tomli-2.0.1.dist-info
C /opt/_internal/tools/lib/python3.10/site-packages/wheel-0.40.0.dist-info
D /opt/_internal/tools/lib/python3.10/site-packages/pip-23.1.1.dist-info
D /opt/_internal/tools/lib/python3.10/site-packages/argcomplete-3.0.8.dist-info
D /opt/_internal/tools/lib/python3.10/site-packages/setuptools-67.7.1.dist-info
A /opt/_internal/pipx/shared/lib/python3.10/site-packages/pip-23.1.dist-info
A /opt/_internal/pipx/shared/lib/python3.10/site-packages/setuptools-67.6.1.dist-info
C /opt/_internal/pipx/shared/lib/python3.10/site-packages/wheel-0.40.0.dist-info
D /opt/_internal/pipx/shared/lib/python3.10/site-packages/setuptools-67.7.2.dist-info
D /opt/_internal/pipx/shared/lib/python3.10/site-packages/pip-23.1.1.dist-info
C /opt/_internal/pipx/venvs/auditwheel/lib/python3.10/site-packages/auditwheel-5.3.0.dist-info
C /opt/_internal/pipx/venvs/auditwheel/lib/python3.10/site-packages/pyelftools-0.29.dist-info
C /opt/_internal/pipx/venvs/cmake/lib/python3.10/site-packages/cmake-3.26.3.dist-info
A /opt/_internal/pipx/venvs/patchelf/lib/python3.10/site-packages/patchelf-0.17.2.1.dist-info
D /opt/_internal/pipx/venvs/patchelf/lib/python3.10/site-packages/patchelf-0.18.0.0.dist-info
C /opt/_internal/pipx/venvs/swig/lib/python3.10/site-packages/swig-4.1.1.dist-info

between these two containers:

Working: quay.io/pypa/manylinux2014_x86_64@sha256:bc1b92cee27af8cd949e6abb7036ec17e2ce66066a89131fdf6ec9212c6762e3
Broken : quay.io/pypa/manylinux2014_x86_64@sha256:d2e6fbda70ff201243e824a86b5ce3dc3f93fa56865d1d84a2a3ac0578c86826

our generated wheels now have the following error when trying to import our modules:

$ venv/bin/python -c "import vtk"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/builds/gitlab-kitware-sciviz-ci/venv/lib/python3.10/site-packages/vtk.py", line 5, in <module>
    from vtkmodules.vtkWebCore import *
ImportError: libXcursor-1a09904e.so.1.0.2: ELF load command address/offset not properly aligned

Something seems to have broken this between 0.17.2.1 and 0.18.0.0.

[mathstuf]

Looking at the logs…it's a bunch of CI chores and a submodule bump. Upstream issue: NixOS/patchelf#492

[SeanCurtis-TRI]

Looks like they're reverting.

[mayeut]

The 0.18.0.0 version has been yanked pending further investigation upstream.