[Debian-med-packaging] Bug#1150529: python-cogent: FTBFS: E sqlite3.OperationalError: unable to open database file

[Santiago Vila]

Package: src:python-cogent
Version: 2026.6.2a0+dfsg-3
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

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

https://people.debian.org/~sanvila/build-logs/202610/

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 cannot 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-cogent, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
/usr/lib/python3/dist-packages/scinexus/sqlite_data_store.py:76: in open_sqlite_db_rw
    db = _connect_sqlite_db_rw(path)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3/dist-packages/scinexus/sqlite_data_store.py:83: in _connect_sqlite_db_rw
    db = sqlite3.connect(
E   sqlite3.OperationalError: unable to open database file
=============================== warnings summary ===============================
../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1624
  /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1624: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead.
    self.args, self.args_source = self._decide_args(

../../../../../../usr/lib/python3/dist-packages/_pytest/python.py:124
  /usr/lib/python3/dist-packages/_pytest/python.py:124: PytestRemovedIn10Warning: Passing a non-Collection iterable to parametrize is deprecated.
  Test: tests/test_evolve/test_coevolution.py::test_joint_entropies, argvalues type: combinations
  Please convert to a list or tuple.
  See https://docs.pytest.org/en/stable/deprecations.html#parametrize-iterators
    metafunc.parametrize(*marker.args, **marker.kwargs, _param_mark=marker)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
ERROR tests/test_app/test_init.py - sqlite3.OperationalError: unable to open ...
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
================== 3 deselected, 2 warnings, 1 error in 8.44s ==================
E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_cogent3/build; python3.14 -m pytest --ignore=test_app/test_plugins.py -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip and not internet and not test_load_from_url '
dh_auto_test: error: pybuild --test -i python{version} -p 3.14 --parallel=1 returned exit code 13
make: *** [debian/rules:30: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
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