Control: retitle -1 python-prodigy: FTBFS: ModuleNotFoundError: No module named
'Bio.PDB.ccealign'
On Fri, Oct 23, 2026 at 04:44:52PM +0000, Santiago Vila wrote:
tests/test_prodigy.py:9: in <module>
from Bio.PDB.Model import Model
/usr/lib/python3/dist-packages/Bio/PDB/__init__.py:30: in <module>
raise MissingPythonDependencyError(
E Bio.MissingPythonDependencyError: Please install NumPy if you want to use
Bio.PDB. See http://www.numpy.org/
Slightly different error now, presumably just waiting on more rebuilds:
I: pybuild base:383: cd
/build/reproducible-path/python-prodigy-2.4.0/.pybuild/cpython3_3.15_prodigy/build;
python3.15 -m pytest tests
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330, in
wrap_session
session.exitstatus = doit(config, session) or 0
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 383, in _main
config.hook.pytest_collection(session=session)
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__
return self._hookexec(self.name, self._hookimpls.copy(), kwargs,
firstresult)
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in
_hookexec
return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in
_multicall
raise exception
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in
_multicall
teardown.throw(exception)
File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 803, in
pytest_collection
return (yield)
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in
_multicall
teardown.throw(exception)
File "/usr/lib/python3/dist-packages/_pytest/warnings.py", line 99, in
pytest_collection
return (yield)
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in
_multicall
teardown.throw(exception)
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 1445,
in pytest_collection
return (yield)
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in
_multicall
res = hook_impl.function(*args)
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 394, in
pytest_collection
session.perform_collect()
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 869, in
perform_collect
self.items.extend(self.genitems(node))
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 1035, in genitems
yield from self.genitems(subnode)
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 1032, in genitems
rep, duplicate = self._collect_one_node(node, handle_dupes)
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 895, in
_collect_one_node
rep = collect_one_node(node)
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 589, in
collect_one_node
rep: CollectReport = ihook.pytest_make_collect_report(collector=collector)
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__
return self._hookexec(self.name, self._hookimpls.copy(), kwargs,
firstresult)
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in
_hookexec
return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in
_multicall
raise exception
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in
_multicall
teardown.throw(exception)
File "/usr/lib/python3/dist-packages/_pytest/fixtures.py", line 1798, in
pytest_make_collect_report
result = yield
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in
_multicall
teardown.throw(exception)
File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in
pytest_make_collect_report
rep = yield
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in
_multicall
res = hook_impl.function(*args)
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 428, in
pytest_make_collect_report
errorinfo = collector.repr_failure(call.excinfo)
File "/usr/lib/python3/dist-packages/_pytest/nodes.py", line 526, in
repr_failure
return self._repr_failure_py(excinfo, style=tbstyle)
File "/usr/lib/python3/dist-packages/_pytest/nodes.py", line 448, in
_repr_failure_py
return excinfo.getrepr(
File "/usr/lib/python3/dist-packages/_pytest/_code/code.py", line 774, in
getrepr
return fmt.repr_excinfo(self)
File "/usr/lib/python3/dist-packages/_pytest/_code/code.py", line 1224, in
repr_excinfo
reprtraceback = self.repr_traceback(excinfo_)
File "/usr/lib/python3/dist-packages/_pytest/_code/code.py", line 1150, in
repr_traceback
self.repr_traceback_entry(entry, excinfo if last == entry else None)
File "/usr/lib/python3/dist-packages/_pytest/_code/code.py", line 1092, in
repr_traceback_entry
s = self.get_source(
File "/usr/lib/python3/dist-packages/_pytest/_code/code.py", line 983, in
get_source
lines.extend(self.get_exconly(excinfo, indent=indent, markall=True))
File "/usr/lib/python3/dist-packages/_pytest/_code/code.py", line 1032, in
get_exconly
exlines = excinfo.exconly(tryshort=True).split("\n")
File "/usr/lib/python3/dist-packages/_pytest/_code/code.py", line 674, in
exconly
lines = format_exception_only(self.value)
File "/usr/lib/python3.15/traceback.py", line 221, in format_exception_only
te = TracebackException(type(value), value, None, compact=True)
File "/usr/lib/python3.15/traceback.py", line 1206, in __init__
elif abi_tag := _find_incompatible_extension_module(module_name):
File "/usr/lib/python3.15/traceback.py", line 2082, in
_find_incompatible_extension_module
traversable = importlib.resources.files(parent)
File "/usr/lib/python3.15/importlib/resources/_common.py", line 22, in files
return from_package(resolve(anchor))
File "/usr/lib/python3.15/functools.py", line 1003, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
File "/usr/lib/python3.15/importlib/resources/_common.py", line 48, in _
return importlib.import_module(cand)
File "/usr/lib/python3.15/importlib/__init__.py", line 88, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1390, in _gcd_import
File "<frozen importlib._bootstrap>", line 1350, in _find_and_load
File "<frozen importlib._bootstrap>", line 1309, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 915, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 751, in exec_module
File "<frozen importlib._bootstrap>", line 549, in _call_with_frames_removed
File "/usr/lib/python3/dist-packages/Bio/PDB/__init__.py", line 40, in
<module>
from .cealign import CEAligner
File "/usr/lib/python3/dist-packages/Bio/PDB/cealign.py", line 23, in <module>
from Bio.PDB.ccealign import run_cealign
ModuleNotFoundError: No module named 'Bio.PDB.ccealign'
Thanks,
--
Colin Watson (he/him) [[email protected]]
