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Python 3.14: Installation from source suddenly stopped working #1262

@benz0li

Description

@benz0li

Until yesterday, PyTables built just fine: https://gitlab.b-data.ch/jupyterlab/python/scipy/-/jobs/213221#L1964

Now, the build fails: https://gitlab.b-data.ch/python/scipy/-/jobs/213699#L1899


Even in an image where it was installed successfully, a reinstallation fails. To reproduce:

On a Linux machine (x86_64, AArch64) with Docker installed

docker run --rm -ti quay.io/bedata/python/scipy:tables bash

(Image quay.io/bedata/python/scipy:tables is no longer available)

In the container

Check version of PyTables:

python -c 'import tables; print(tables.get_pytables_version())'
3.10.2

Uninstall + reinstall:

pip uninstall -y tables; pip install tables
Found existing installation: tables 3.10.2
Uninstalling tables-3.10.2:
  Successfully uninstalled tables-3.10.2
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
Collecting tables
  Downloading tables-3.10.2.tar.gz (4.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 42.9 MB/s  0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [49 lines of output]
      /tmp/lzo_version_datei5ec3d_x.c:1:10: fatal error: lzo/lzo1x.h: No such file or directory
          1 | #include "lzo/lzo1x.h"
            |          ^~~~~~~~~~~~~
      compilation terminated.
      /tmp/lzo_version_datevry85lcd.c:1:10: fatal error: lzo1x.h: No such file or directory
          1 | #include "lzo1x.h"
            |          ^~~~~~~~~
      compilation terminated.
      /tmp/BZ2_bzlibVersionfny6co47.c:1:10: fatal error: bzlib.h: No such file or directory
          1 | #include "bzlib.h"
            |          ^~~~~~~~~
      compilation terminated.
      /tmp/blosc_list_compressorsdqjl3ov5.c:1:10: fatal error: blosc.h: No such file or directory
          1 | #include "blosc.h"
            |          ^~~~~~~~~
      compilation terminated.
      * Using Python 3.14.0 (main, Oct  8 2025, 21:27:27) [GCC 14.2.0]
      * Found cython 3.1.6
      * USE_PKGCONFIG: True
      * pkg-config header dirs for HDF5: /usr/include/hdf5/serial
      * pkg-config library dirs for HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial
      * Found HDF5 headers at ``/usr/include/hdf5/serial``, library at ``/usr/lib/x86_64-linux-gnu/hdf5/serial``.
      * Could not find a local LZO 2 installation headers (hdrdir=None) and/or libdir (libdir=False); disabling support for it.
      * Could not find a local LZO 1 installation headers (hdrdir=None) and/or libdir (libdir=False); disabling support for it.
      * Could not find a local bzip2 installation headers (hdrdir=None) and/or libdir (libdir=False); disabling support for it.
      * Could not find a local blosc installation headers (hdrdir=None) and/or libdir (libdir=False); using internal sources.
      * Run 'blosc2_find_directories_hook'
      * Found blosc2 headers at ``/tmp/pip-build-env-0w6ws20g/overlay/lib/python3.14/site-packages/include``, library at ``/tmp/pip-build-env-0w6ws20g/overlay/lib/python3.14/site-packages/lib64``.
      Traceback (most recent call last):
        File "/usr/local/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
          ~~~~^^
        File "/usr/local/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
        File "/usr/local/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 143, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/tmp/pip-build-env-0w6ws20g/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 331, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-0w6ws20g/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 301, in _get_build_requires
          self.run_setup()
          ~~~~~~~~~~~~~~^^
        File "/tmp/pip-build-env-0w6ws20g/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
          ~~~~^^^^^^^^^^^^^^^^
        File "<string>", line 931, in <module>
        File "<string>", line 89, in get_blosc2_version
      ValueError: invalid literal for int() with base 10: '1.dev'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.

[notice] A new release of pip is available: 25.2 -> 25.3
[notice] To update, run: pip install --upgrade pip
error: subprocess-exited-with-error

× Getting requirements to build wheel 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.

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