Bug#1143376: pytorch-geometric: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.14 --parallel=2 returned exit code 13

Santiago Vila sanvila at debian.org
Sat Aug 1 23:37:54 BST 2026 

Package: src:pytorch-geometric
Version: 2.8.0-1
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/202608/

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:pytorch-geometric, 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
   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:142: Building wheel for python3.14 with "build" module
I: pybuild base:385: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric  
* Building wheel...
Successfully built torch_geometric-2.8.0-py3-none-any.whl

[... snipped ...]

      self._context.run(self.run)
      ~~~~~~~~~~~~~~~~~^^^^^^^^^^
    File "/usr/lib/python3.14/threading.py", line 1024, in run
      self._target(*self._args, **self._kwargs)
      ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/lib/python3.14/multiprocessing/queues.py", line 289, in _feed
      queue_sem.release()
      ~~~~~~~~~~~~~~~~~^^
  ValueError: semaphore or lock released too many times
  
  Enable tracemalloc to get traceback where the object was allocated.
  See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
    warnings.warn(pytest.PytestUnhandledThreadExceptionWarning(msg))

test/nn/aggr/test_multi.py: 10 warnings
test/nn/dense/test_linear.py: 1 warning
test/nn/test_sequential.py: 1 warning
  /usr/lib/python3.14/ast.py:506: UserWarning: The TorchScript type system doesn't support instance-level annotations on empty non-base types in `__init__`. Instead, either 1) use a type annotation in the class body, or 2) wrap the type in `torch.jit.Attribute`.
    return visitor(node)

test/nn/dense/test_linear.py::test_hetero_linear_amp[None-cpu]
test/nn/dense/test_linear.py::test_hetero_linear_amp[True-cpu]
test/nn/dense/test_linear.py::test_hetero_linear_amp[False-cpu]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/nn/dense/test_linear.py:173: UserWarning: CUDA is not available or torch_xla is imported. Disabling autocast.
    with torch.amp.autocast('cuda'):

test/profile/test_profiler.py::test_profiler[cpu]
  /usr/lib/python3/dist-packages/torch/profiler/profiler.py:272: UserWarning: Warning: Profiler clears events at the end of each cycle.Only events from the current cycle will be reported.To keep events across cycles, set acc_events=True.
    _warn_once(

test/test_edge_index.py::test_data_loader[True-2-int64]
test/test_edge_index.py::test_data_loader[True-2-int32]
test/test_hash_tensor.py::test_data_loader[True-2]
test/test_index.py::test_data_loader[True-2-int64]
test/test_index.py::test_data_loader[True-2-int32]
  /usr/lib/python3/dist-packages/torch/utils/data/dataloader.py:1095: UserWarning: 'pin_memory' argument is set as true but no accelerator is found, then device pinned memory won't be used.
    super().__init__(loader)

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: Encountered known ONNX serialization issue (Exception). This is likely the allowzero boolean attribute bug. Attempting workaround...
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: Retrying ONNX export with opset_version=17
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: Retrying ONNX export with opset_version=16
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: Retrying ONNX export with opset_version=15
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: Retrying ONNX export with opset_version=14
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: Retrying ONNX export with opset_version=13
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: Retrying ONNX export with opset_version=11
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: Retrying ONNX export with legacy settings (dynamo=False, opset_version=11)
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: Retrying ONNX export with minimal settings as last resort
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_safe_onnx_export_with_skip_on_error
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:120: UserWarning: ONNX export skipped due to known upstream issue (onnx_ir.serde.SerdeError). This is caused by a bug in the onnx_ir package where boolean allowzero attributes cannot be serialized. All workarounds failed. Consider updating packages: pip install --upgrade onnx onnxscript onnx_ir
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: Encountered known ONNX serialization issue (Exception). This is likely the allowzero boolean attribute bug. Attempting workaround...
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: Retrying ONNX export with opset_version=17
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: Retrying ONNX export with opset_version=16
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: Retrying ONNX export with opset_version=15
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: Retrying ONNX export with opset_version=14
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: Retrying ONNX export with opset_version=13
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: Retrying ONNX export with opset_version=11
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: Retrying ONNX export with legacy settings (dynamo=False, opset_version=11)
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: Retrying ONNX export with minimal settings as last resort
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_serde_error_patterns
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:156: UserWarning: ONNX export skipped due to known upstream issue (onnx_ir.serde.SerdeError). This is caused by a bug in the onnx_ir package where boolean allowzero attributes cannot be serialized. All workarounds failed. Consider updating packages: pip install --upgrade onnx onnxscript onnx_ir
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_dynamo_fallback
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:219: UserWarning: Encountered known ONNX serialization issue (Exception). This is likely the allowzero boolean attribute bug. Attempting workaround...
    result = safe_onnx_export(model, (x, ), f.name, dynamo=True)

test/test_onnx.py::test_dynamo_fallback
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:219: UserWarning: Retrying ONNX export with dynamo=False as workaround
    result = safe_onnx_export(model, (x, ), f.name, dynamo=True)

test/test_onnx.py::test_opset_fallback
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:254: UserWarning: Encountered known ONNX serialization issue (Exception). This is likely the allowzero boolean attribute bug. Attempting workaround...
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_opset_fallback
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:254: UserWarning: Retrying ONNX export with opset_version=17
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:286: UserWarning: Encountered known ONNX serialization issue (Exception). This is likely the allowzero boolean attribute bug. Attempting workaround...
    safe_onnx_export(model, (x, ), f.name, skip_on_error=False)

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:286: UserWarning: Retrying ONNX export with opset_version=17
    safe_onnx_export(model, (x, ), f.name, skip_on_error=False)

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:286: UserWarning: Retrying ONNX export with opset_version=16
    safe_onnx_export(model, (x, ), f.name, skip_on_error=False)

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:286: UserWarning: Retrying ONNX export with opset_version=15
    safe_onnx_export(model, (x, ), f.name, skip_on_error=False)

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:286: UserWarning: Retrying ONNX export with opset_version=14
    safe_onnx_export(model, (x, ), f.name, skip_on_error=False)

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:286: UserWarning: Retrying ONNX export with opset_version=13
    safe_onnx_export(model, (x, ), f.name, skip_on_error=False)

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:286: UserWarning: Retrying ONNX export with opset_version=11
    safe_onnx_export(model, (x, ), f.name, skip_on_error=False)

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:286: UserWarning: Retrying ONNX export with legacy settings (dynamo=False, opset_version=11)
    safe_onnx_export(model, (x, ), f.name, skip_on_error=False)

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:286: UserWarning: Retrying ONNX export with minimal settings as last resort
    safe_onnx_export(model, (x, ), f.name, skip_on_error=False)

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: Encountered known ONNX serialization issue (Exception). This is likely the allowzero boolean attribute bug. Attempting workaround...
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: Retrying ONNX export with opset_version=17
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: Retrying ONNX export with opset_version=16
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: Retrying ONNX export with opset_version=15
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: Retrying ONNX export with opset_version=14
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: Retrying ONNX export with opset_version=13
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: Retrying ONNX export with opset_version=11
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: Retrying ONNX export with legacy settings (dynamo=False, opset_version=11)
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: Retrying ONNX export with minimal settings as last resort
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_all_strategies_fail
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:289: UserWarning: ONNX export skipped due to known upstream issue (onnx_ir.serde.SerdeError). This is caused by a bug in the onnx_ir package where boolean allowzero attributes cannot be serialized. All workarounds failed. Consider updating packages: pip install --upgrade onnx onnxscript onnx_ir
    result = safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_pytest_environment_detection
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:318: UserWarning: Encountered known ONNX serialization issue (Exception). This is likely the allowzero boolean attribute bug. Attempting workaround...
    safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_pytest_environment_detection
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:318: UserWarning: Retrying ONNX export with opset_version=17
    safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_pytest_environment_detection
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:318: UserWarning: Retrying ONNX export with opset_version=16
    safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_pytest_environment_detection
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:318: UserWarning: Retrying ONNX export with opset_version=15
    safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_pytest_environment_detection
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:318: UserWarning: Retrying ONNX export with opset_version=14
    safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_pytest_environment_detection
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:318: UserWarning: Retrying ONNX export with opset_version=13
    safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_pytest_environment_detection
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:318: UserWarning: Retrying ONNX export with opset_version=11
    safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_pytest_environment_detection
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:318: UserWarning: Retrying ONNX export with legacy settings (dynamo=False, opset_version=11)
    safe_onnx_export(model, (x, ), f.name,

test/test_onnx.py::test_pytest_environment_detection
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build/test/test_onnx.py:318: UserWarning: Retrying ONNX export with minimal settings as last resort
    safe_onnx_export(model, (x, ), f.name,

test/test_warnings.py::test_warning_cache
  /usr/lib/python3/dist-packages/pluggy/_callers.py:121: UserWarning: test
    res = hook_impl.function(*args)

test/test_warnings.py::test_warning_cache
  /usr/lib/python3/dist-packages/pluggy/_callers.py:121: UserWarning: test2
    res = hook_impl.function(*args)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED test/loader/test_dataloader.py::test_dataloader_on_disk_dataset[2] - TypeError: cannot pickle 'sqlite3.Connection' object
when serializing dict item '_connection'
when serializing torch_geometric.data.database.SQLiteDatabase state
when serializing torch_geometric.data.database.SQLiteDatabase object
when serializing dict item '_db'
when serializing torch_geometric.data.on_disk_dataset.OnDiskDataset state
when serializing torch_geometric.data.on_disk_dataset.OnDiskDataset object
when serializing tuple item 1
when serializing dict item '_args'
when serializing multiprocessing.context.Process state
when serializing multiprocessing.context.Process object
FAILED test/nn/conv/utils/test_gnn_cheatsheet.py::test_gnn_cheatsheet - AssertionError: assert False
 +  where False = <function supports_bipartite_graphs at 0x7fedbe645a60>('SAGEConv')
 +    where <function supports_bipartite_graphs at 0x7fedbe645a60> = utils.supports_bipartite_graphs
FAILED test/test_config_store.py::test_to_dataclass - AttributeError: readonly attribute
FAILED test/test_config_store.py::test_register - AttributeError: readonly attribute
FAILED test/test_config_store.py::test_fill_config_store - AttributeError: readonly attribute
= 5 failed, 6001 passed, 862 skipped, 263 deselected, 1 xfailed, 1 xpassed, 131 warnings in 149.14s (0:02:29) =
E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_torch-geometric/build; python3.14 -m pytest -k 'not test_citeseer and not test_enzymes and not test_mutag and not _on_cora and not test_asap and not test_feature_store and not test_two_hop and not test_graph_unet and not test_spspmm and not test_add_metapaths and not test_type_repr and not test_protein_mpnn_dataset and not neighbor_sampler'
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.14 --parallel=2 returned exit code 13
make: *** [debian/rules:21: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
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