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

Package:
src:pytorch-geometric
Source:
src:pytorch-geometric
Submitter:
Santiago Vila
Date:
2026-10-14 10:21:03 UTC
Severity:
normal
Tags:
#1143376#5
Date:
2026-08-01 22:37:54 UTC
From:
To:
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)
#1143376#10
Date:
2026-10-14 10:19:34 UTC
From:
To:
We believe that the bug you reported is fixed in the latest version of
pytorch-geometric, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1143376@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andrius Merkys <merkys@debian.org> (supplier of updated pytorch-geometric package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 14 Oct 2026 05:25:42 -0400
Source: pytorch-geometric
Architecture: source
Version: 2.8.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Deep Learning Team <debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Closes: 1143376 1149011
Changes:
 pytorch-geometric (2.8.1-1) unstable; urgency=medium
 .
   [ Alexandre Detiste ]
   * build-depends on python3-flit instead of the whole 'flit' toolbox
     (Closes: #1149011)
   * drop 'Rules-Requires-Root: no': it is now the default
   * mark python3-setuptools as nocheck, this build with Flit
   * rewrite d/watch in v5 format
   * bump Standards-Version to 4.7.4, drop Priority: tag
   * Salsa CI: disable useless ALL & ANY, enable nocheck
 .
   [ Andrius Merkys ]
   * New upstream version 2.8.1
   * Ignore test_dataloader_on_disk_dataset and test_gnn_cheatsheet
     (Closes: #1143376)
Checksums-Sha1:
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 e8e8b552f38664976dcffede9c1a8a37d30ca53e 4253971 pytorch-geometric_2.8.1.orig.tar.gz
 7e5063d038ce72139c75bddb598a23db62b0472f 11656 pytorch-geometric_2.8.1-1.debian.tar.xz
 7098014e58e8662a2ab9abbc0d47b4c4a36584f3 5613 pytorch-geometric_2.8.1-1_source.buildinfo
Checksums-Sha256:
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