[Debian-med-packaging] Bug#1116850: python-bx: FTBFS with the nocheck build profile

[Santiago Vila]

Package: src:python-bx
Version: 0.13.0-1
Severity: important
Tags: forky sid ftbfs
User: debian-qa at lists.debian.org
Usertags: ftbfs-nocheck-profile

Dear maintainer:

During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:

https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck

(It's a wiki, so you are welcome to contribute)

[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:python-bx, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
   debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
find -name "*.pyx" | sed 's/pyx$/c/' | xargs rm -f
grep -rli "Generated by Cython" lib/ | xargs -r rm
rm -rf lib/bx_python.egg-info
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
   dh_auto_build -O--buildsystem=pybuild
I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module
I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_bx-python  
* Building wheel...
Traceback (most recent call last):
  File "<string>", line 26, in main
ModuleNotFoundError: No module named 'numpy'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
    main()
    ~~~~^^
  File "/usr/lib/python3/dist-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in main
    json_out["return_val"] = hook(**hook_input["kwargs"])
                             ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
    return _build_backend().build_wheel(
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
        wheel_directory, config_settings, metadata_directory
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 435, in build_wheel
    return _build(['bdist_wheel'])
  File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 426, in _build
    return self._build_with_temp_dir(
           ~~~~~~~~~~~~~~~~~~~~~~~~~^
        cmd,
        ^^^^
    ...<3 lines>...
        self._arbitrary_args(config_settings),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir
    self.run_setup()
    ~~~~~~~~~~~~~~^^
  File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 320, in run_setup
    exec(code, locals())
    ~~~~^^^^^^^^^^^^^^^^
  File "<string>", line 150, in <module>
  File "<string>", line 31, in main
Exception: numpy must be installed to build: No module named 'numpy'

ERROR Backend subprocess exited when trying to invoke build_wheel
E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_bx-python  
dh_auto_build: error: pybuild --build -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:13: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------