Bug#1114329: python-rioxarray: FTBFS: ..Fatal Python error: Segmentation fault

Santiago Vila sanvila at debian.org
Fri Sep 5 19:24:43 BST 2025 

Package: src:python-rioxarray
Version: 0.19.0-1
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, 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/

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:python-rioxarray, 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:129: Building wheel for python3.13 with "build" module
I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_rioxarray  
* Building wheel...
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
!!

        ********************************************************************************
        Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

        By 2026-Feb-18, you need to update your project and remove deprecated calls
        or your builds will no longer be supported.

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  corresp(dist, value, root_dir)
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!

        ********************************************************************************
        Please consider removing the following classifiers in favor of a SPDX license expression:

        License :: OSI Approved :: Apache Software License

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  dist._finalize_license_expression()
/usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!

        ********************************************************************************
        Please consider removing the following classifiers in favor of a SPDX license expression:

        License :: OSI Approved :: Apache Software License

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  self._finalize_license_expression()
running bdist_wheel
running build
running build_py
creating build/lib/rioxarray
copying rioxarray/rioxarray.py -> build/lib/rioxarray
copying rioxarray/exceptions.py -> build/lib/rioxarray
copying rioxarray/_io.py -> build/lib/rioxarray
copying rioxarray/_options.py -> build/lib/rioxarray
copying rioxarray/xarray_plugin.py -> build/lib/rioxarray
copying rioxarray/crs.py -> build/lib/rioxarray
copying rioxarray/raster_writer.py -> build/lib/rioxarray
copying rioxarray/merge.py -> build/lib/rioxarray
copying rioxarray/raster_dataset.py -> build/lib/rioxarray
copying rioxarray/raster_array.py -> build/lib/rioxarray
copying rioxarray/_show_versions.py -> build/lib/rioxarray
copying rioxarray/__init__.py -> build/lib/rioxarray
running egg_info
creating rioxarray.egg-info
writing rioxarray.egg-info/PKG-INFO
writing dependency_links to rioxarray.egg-info/dependency_links.txt
writing entry points to rioxarray.egg-info/entry_points.txt
writing requirements to rioxarray.egg-info/requires.txt
writing top-level names to rioxarray.egg-info/top_level.txt
writing manifest file 'rioxarray.egg-info/SOURCES.txt'
reading manifest file 'rioxarray.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*' found under directory 'test'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
no previously-included directories found matching 'docs'
adding license file 'LICENSE'
adding license file 'LICENSE_datacube'
adding license file 'LICENSE_xarray'
adding license file 'AUTHORS.rst'
writing manifest file 'rioxarray.egg-info/SOURCES.txt'
copying rioxarray/py.typed -> build/lib/rioxarray
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/rioxarray
copying build/lib/rioxarray/rioxarray.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/exceptions.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/_io.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/_options.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/xarray_plugin.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/py.typed -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/crs.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/raster_writer.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/merge.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/raster_dataset.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/raster_array.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/_show_versions.py -> build/bdist.linux-x86_64/wheel/./rioxarray
copying build/lib/rioxarray/__init__.py -> build/bdist.linux-x86_64/wheel/./rioxarray
running install_egg_info
Copying rioxarray.egg-info to build/bdist.linux-x86_64/wheel/./rioxarray-0.19.0.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/rioxarray-0.19.0.dist-info/WHEEL
creating '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_rioxarray/.tmp-s2ogz_17/rioxarray-0.19.0-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'rioxarray/__init__.py'
adding 'rioxarray/_io.py'
adding 'rioxarray/_options.py'
adding 'rioxarray/_show_versions.py'
adding 'rioxarray/crs.py'
adding 'rioxarray/exceptions.py'
adding 'rioxarray/merge.py'
adding 'rioxarray/py.typed'
adding 'rioxarray/raster_array.py'
adding 'rioxarray/raster_dataset.py'
adding 'rioxarray/raster_writer.py'
adding 'rioxarray/rioxarray.py'
adding 'rioxarray/xarray_plugin.py'
adding 'rioxarray-0.19.0.dist-info/licenses/AUTHORS.rst'
adding 'rioxarray-0.19.0.dist-info/licenses/LICENSE'
adding 'rioxarray-0.19.0.dist-info/licenses/LICENSE_datacube'
adding 'rioxarray-0.19.0.dist-info/licenses/LICENSE_xarray'
adding 'rioxarray-0.19.0.dist-info/METADATA'
adding 'rioxarray-0.19.0.dist-info/WHEEL'
adding 'rioxarray-0.19.0.dist-info/entry_points.txt'
adding 'rioxarray-0.19.0.dist-info/top_level.txt'
adding 'rioxarray-0.19.0.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built rioxarray-0.19.0-py3-none-any.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module
   dh_auto_test -O--buildsystem=pybuild
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_rioxarray/build; python3.13 -m pytest -k "not test_clip_geojson__no_drop and not test_clip_geojson and not test_interpolate_na and not test_merge_datasets and not test_open_rasterio_mask_chunk_clip and not test_to_raster__different_dtype and not test_nonstandard_dims_write_coordinate_system__projected_ft"
============================= test session starts ==============================
platform linux -- Python 3.13.7, pytest-8.4.1, pluggy-1.6.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_rioxarray/build
configfile: pyproject.toml
plugins: cov-5.0.0, timeout-2.3.1, typeguard-4.4.4
collected 495 items / 44 deselected / 451 selected

test/integration/test_integration__io.py ............................... [  6%]
..Fatal Python error: Segmentation fault

Current thread 0x00007f9ebf32f6c0 (most recent call first):
  Garbage-collecting
  File "/usr/lib/python3/dist-packages/xarray/backends/file_manager.py", line 234 in close
  File "/usr/lib/python3/dist-packages/xarray/backends/file_manager.py", line 250 in __del__
  File "/usr/lib/python3/dist-packages/dask/order.py", line 267 in _with_offset
  File "/usr/lib/python3/dist-packages/dask/order.py", line 284 in order
  File "/usr/lib/python3/dist-packages/dask/_task_spec.py", line 981 in execute_graph
  File "/usr/lib/python3/dist-packages/dask/_task_spec.py", line 171 in _execute_subgraph
  File "/usr/lib/python3/dist-packages/dask/_task_spec.py", line 745 in __call__
  File "/usr/lib/python3/dist-packages/dask/local.py", line 229 in execute_task
  File "/usr/lib/python3/dist-packages/dask/local.py", line 243 in batch_execute_tasks
  File "/usr/lib/python3.13/concurrent/futures/thread.py", line 59 in run
  File "/usr/lib/python3.13/concurrent/futures/thread.py", line 93 in _worker
  File "/usr/lib/python3.13/threading.py", line 994 in run
  File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner
  File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap

Thread 0x00007f9ebfb306c0 (most recent call first):
  File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker
  File "/usr/lib/python3.13/threading.py", line 994 in run
  File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner
  File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap

Thread 0x00007f9ed4222100 (most recent call first):
  File "/usr/lib/python3.13/threading.py", line 359 in wait
  File "/usr/lib/python3.13/queue.py", line 199 in get
  File "/usr/lib/python3/dist-packages/dask/local.py", line 140 in queue_get
  File "/usr/lib/python3/dist-packages/dask/local.py", line 505 in get_async
  File "/usr/lib/python3/dist-packages/dask/threaded.py", line 91 in get
  File "/usr/lib/python3/dist-packages/dask/base.py", line 660 in compute
  File "/usr/lib/python3/dist-packages/dask/base.py", line 372 in compute
  File "/usr/lib/python3/dist-packages/dask/array/core.py", line 1876 in __bool__
  File "/usr/lib/python3/dist-packages/xarray/core/duck_array_ops.py", line 346 in allclose_or_equiv
  File "/usr/lib/python3/dist-packages/xarray/testing/assertions.py", line 51 in _data_allclose_or_equiv
  File "/usr/lib/python3/dist-packages/xarray/testing/assertions.py", line 240 in compat_variable
  File "/usr/lib/python3/dist-packages/xarray/testing/assertions.py", line 248 in assert_allclose
  File "/usr/lib/python3/dist-packages/xarray/testing/assertions.py", line 32 in wrapper
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_rioxarray/build/test/integration/test_integration__io.py", line 502 in _check_raster
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_rioxarray/build/test/integration/test_integration__io.py", line 519 in test_band_as_variable
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 157 in pytest_pyfunc_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1671 in runtest
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 178 in pytest_runtest_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 246 in <lambda>
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 344 in from_call
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245 in call_and_report
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 136 in runtestprotocol
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 117 in pytest_runtest_protocol
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 367 in pytest_runtestloop
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 343 in _main
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 289 in wrap_session
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 336 in pytest_cmdline_main
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main
  File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in <module>
  File "<frozen runpy>", line 88 in _run_code
  File "<frozen runpy>", line 198 in _run_module_as_main

Extension modules: rasterio._err, rasterio._filepath, raster [too-long-redacted] , netCDF4._netCDF4 (total: 111)
Segmentation fault
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=139: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_rioxarray/build; python3.13 -m pytest -k "not test_clip_geojson__no_drop and not test_clip_geojson and not test_interpolate_na and not test_merge_datasets and not test_open_rasterio_mask_chunk_clip and not test_to_raster__different_dtype and not test_nonstandard_dims_write_coordinate_system__projected_ft"
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:20: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

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