[Debian-med-packaging] Bug#1116912: seqmagick: FTBFS with the nocheck build profile

[Santiago Vila]

Package: src:seqmagick
Version: 0.8.6-3
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:seqmagick, so that this is still
visible in the BTS web page for this package.

Thanks.

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[...]
 debian/rules clean
dh clean --with python3 --buildsystem=pybuild
   debian/rules execute_before_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p seqmagick/data
echo 0.8.6 > seqmagick/data/ver
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py clean 
/usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  dist.fetch_build_eggs(dist.setup_requires)
/usr/bin/python3.13: No module named pip
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/setuptools/installer.py", line 107, in _fetch_build_egg_no_warn
    subprocess.check_call(cmd)
    ~~~~~~~~~~~~~~~~~~~~~^^^^^
  File "/usr/lib/python3.13/subprocess.py", line 419, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/usr/bin/python3.13', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmppbpwl2_3', '--quiet', 'pytest>=6.0']' returned non-zero exit status 1.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/setup.py", line 18, in <module>
    setup(name='seqmagick',
    ~~~~~^^^^^^^^^^^^^^^^^^
          version=__version__,
          ^^^^^^^^^^^^^^^^^^^^
    ...<27 lines>...
          ],
          ^^
          license="GPL V3")
          ^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 116, in setup
    _install_setup_requires(attrs)
    ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 89, in _install_setup_requires
    _fetch_build_eggs(dist)
    ~~~~~~~~~~~~~~~~~^^^^^^
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 94, in _fetch_build_eggs
    dist.fetch_build_eggs(dist.setup_requires)
    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 768, in fetch_build_eggs
    return _fetch_build_eggs(self, requires)
  File "/usr/lib/python3/dist-packages/setuptools/installer.py", line 44, in _fetch_build_eggs
    resolved_dists = pkg_resources.working_set.resolve(
        _reqs.parse(requires, pkg_resources.Requirement),  # required for compatibility
        installer=partial(_fetch_build_egg_no_warn, dist),  # avoid warning twice
        replace_conflicting=True,
    )
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 893, in resolve
    dist = self._resolve_dist(
        req, best, replace_conflicting, env, installer, required_by, to_activate
    )
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 929, in _resolve_dist
    dist = best[req.key] = env.best_match(
                           ~~~~~~~~~~~~~~^
        req, ws, installer, replace_conflicting=replace_conflicting
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1267, in best_match
    return self.obtain(req, installer)
           ~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1303, in obtain
    return installer(requirement) if installer else None
           ~~~~~~~~~^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/setuptools/installer.py", line 109, in _fetch_build_egg_no_warn
    raise DistutilsError(str(e)) from e
distutils.errors.DistutilsError: Command '['/usr/bin/python3.13', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmppbpwl2_3', '--quiet', 'pytest>=6.0']' returned non-zero exit status 1.
E: pybuild pybuild:389: clean: plugin distutils failed with: exit code=1: python3.13 setup.py clean 
dh_auto_clean: error: pybuild --clean -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:6: clean] Error 25
dpkg-buildpackage: error: debian/rules clean subprocess returned exit status 2
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