Your message dated Fri, 28 Nov 2025 16:04:37 +0100
with message-id <[email protected]>
and subject line python-rioxarray: FTBFS: ..Fatal Python error: Segmentation
fault
has caused the Debian Bug report #1114329,
regarding python-rioxarray: FTBFS: ..Fatal Python error: Segmentation fault
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1114329: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114329
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Control: severity -1 normal
The segfault is fixed with hdf4 (4.3.1-2).
The package still FTBFS due to test failures likely caused by changes in
rasterio, this is fixed in 0.20.0 in git which lacks the upstream tag on Salsa.
Kind Regards,
Bas
--
PGP Key ID: 4096R/6750F10AE88D4AF1
Fingerprint: 8182 DE41 7056 408D 6146 50D1 6750 F10A E88D 4AF1
--- End Message ---
