Bug#1116779: libpysal: FTBFS with the nocheck build profile

Santiago Vila sanvila at debian.org
Tue Sep 30 15:50:38 BST 2025 

Package: src:libpysal
Version: 4.12.1-1
Severity: important
Tags: forky sid ftbfs
User: debian-qa at lists.debian.org
Usertags: ftbfs-nocheck-profile

Dear maintainer:

During a rebuild of all packages in unstable using the nocheck build profile,
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/

A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:

https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck

(It's a wiki, so you are welcome to contribute)

[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].

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:libpysal, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --sphinxdoc  --buildsystem=pybuild
   dh_auto_clean -O--sphinxdoc -O--buildsystem=pybuild

[... snipped ...]

copying build/lib/libpysal/graph/tests/test_contiguity.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/tests
copying build/lib/libpysal/graph/tests/test_triangulation.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/tests
copying build/lib/libpysal/graph/tests/test_set_ops.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/tests
copying build/lib/libpysal/graph/tests/test_kernel.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/tests
copying build/lib/libpysal/graph/tests/test_base.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/tests
copying build/lib/libpysal/graph/tests/test_plotting.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/tests
copying build/lib/libpysal/graph/tests/test_spatial_lag.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/tests
copying build/lib/libpysal/graph/tests/test_indices.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/tests
copying build/lib/libpysal/graph/tests/test_summary.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/tests
copying build/lib/libpysal/graph/_plotting.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_triangulation.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
creating build/bdist.linux-x86_64/wheel/libpysal/graph/io
copying build/lib/libpysal/graph/io/_parquet.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/io
copying build/lib/libpysal/graph/io/_gal.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/io
copying build/lib/libpysal/graph/io/_gwt.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph/io
copying build/lib/libpysal/graph/base.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_summary.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_indices.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_spatial_lag.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_kernel.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_set_ops.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_raster.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_utils.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_network.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_contiguity.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
copying build/lib/libpysal/graph/_matching.py -> build/bdist.linux-x86_64/wheel/./libpysal/graph
creating build/bdist.linux-x86_64/wheel/libpysal/cg
copying build/lib/libpysal/cg/__init__.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
copying build/lib/libpysal/cg/shapely_ext.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
creating build/bdist.linux-x86_64/wheel/libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_sphere.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_voronoi.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_segmentLocator.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_ashapes.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_locators.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_shapes.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_polygonQuadTreeStructure.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_standalone.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_rtree.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/tests/test_geoJSON.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/tests
copying build/lib/libpysal/cg/kdtree.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
copying build/lib/libpysal/cg/sphere.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
copying build/lib/libpysal/cg/alpha_shapes.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
copying build/lib/libpysal/cg/polygonQuadTreeStructure.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
copying build/lib/libpysal/cg/voronoi.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
copying build/lib/libpysal/cg/segmentLocator.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
copying build/lib/libpysal/cg/standalone.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
copying build/lib/libpysal/cg/rtree.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
creating build/bdist.linux-x86_64/wheel/libpysal/cg/ops
copying build/lib/libpysal/cg/ops/__init__.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/ops
creating build/bdist.linux-x86_64/wheel/libpysal/cg/ops/tests
copying build/lib/libpysal/cg/ops/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/ops/tests
copying build/lib/libpysal/cg/ops/tests/test_tabular.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/ops/tests
copying build/lib/libpysal/cg/ops/tests/test_shapely.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/ops/tests
copying build/lib/libpysal/cg/ops/tests/test_accessors.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/ops/tests
copying build/lib/libpysal/cg/ops/tabular.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/ops
copying build/lib/libpysal/cg/ops/_accessors.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/ops
copying build/lib/libpysal/cg/ops/_shapely.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/ops
copying build/lib/libpysal/cg/ops/atomic.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg/ops
copying build/lib/libpysal/cg/shapes.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
copying build/lib/libpysal/cg/locators.py -> build/bdist.linux-x86_64/wheel/./libpysal/cg
running install_egg_info
Copying libpysal.egg-info to build/bdist.linux-x86_64/wheel/./libpysal-4.12.1.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/libpysal-4.12.1.dist-info/WHEEL
creating '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_libpysal/.tmp-obs3t8er/libpysal-4.12.1-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'libpysal/__init__.py'
adding 'libpysal/common.py'
adding 'libpysal/cg/__init__.py'
adding 'libpysal/cg/alpha_shapes.py'
adding 'libpysal/cg/kdtree.py'
adding 'libpysal/cg/locators.py'
adding 'libpysal/cg/polygonQuadTreeStructure.py'
adding 'libpysal/cg/rtree.py'
adding 'libpysal/cg/segmentLocator.py'
adding 'libpysal/cg/shapely_ext.py'
adding 'libpysal/cg/shapes.py'
adding 'libpysal/cg/sphere.py'
adding 'libpysal/cg/standalone.py'
adding 'libpysal/cg/voronoi.py'
adding 'libpysal/cg/ops/__init__.py'
adding 'libpysal/cg/ops/_accessors.py'
adding 'libpysal/cg/ops/_shapely.py'
adding 'libpysal/cg/ops/atomic.py'
adding 'libpysal/cg/ops/tabular.py'
adding 'libpysal/cg/ops/tests/__init__.py'
adding 'libpysal/cg/ops/tests/test_accessors.py'
adding 'libpysal/cg/ops/tests/test_shapely.py'
adding 'libpysal/cg/ops/tests/test_tabular.py'
adding 'libpysal/cg/tests/__init__.py'
adding 'libpysal/cg/tests/test_ashapes.py'
adding 'libpysal/cg/tests/test_geoJSON.py'
adding 'libpysal/cg/tests/test_locators.py'
adding 'libpysal/cg/tests/test_polygonQuadTreeStructure.py'
adding 'libpysal/cg/tests/test_rtree.py'
adding 'libpysal/cg/tests/test_segmentLocator.py'
adding 'libpysal/cg/tests/test_shapes.py'
adding 'libpysal/cg/tests/test_sphere.py'
adding 'libpysal/cg/tests/test_standalone.py'
adding 'libpysal/cg/tests/test_voronoi.py'
adding 'libpysal/examples/__init__.py'
adding 'libpysal/examples/base.py'
adding 'libpysal/examples/builtin.py'
adding 'libpysal/examples/remotes.py'
adding 'libpysal/examples/tests/__init__.py'
adding 'libpysal/examples/tests/test_available.py'
adding 'libpysal/graph/__init__.py'
adding 'libpysal/graph/_contiguity.py'
adding 'libpysal/graph/_indices.py'
adding 'libpysal/graph/_kernel.py'
adding 'libpysal/graph/_matching.py'
adding 'libpysal/graph/_network.py'
adding 'libpysal/graph/_plotting.py'
adding 'libpysal/graph/_raster.py'
adding 'libpysal/graph/_set_ops.py'
adding 'libpysal/graph/_spatial_lag.py'
adding 'libpysal/graph/_summary.py'
adding 'libpysal/graph/_triangulation.py'
adding 'libpysal/graph/_utils.py'
adding 'libpysal/graph/base.py'
adding 'libpysal/graph/io/_gal.py'
adding 'libpysal/graph/io/_gwt.py'
adding 'libpysal/graph/io/_parquet.py'
adding 'libpysal/graph/tests/test_base.py'
adding 'libpysal/graph/tests/test_builders.py'
adding 'libpysal/graph/tests/test_contiguity.py'
adding 'libpysal/graph/tests/test_indices.py'
adding 'libpysal/graph/tests/test_kernel.py'
adding 'libpysal/graph/tests/test_matching.py'
adding 'libpysal/graph/tests/test_plotting.py'
adding 'libpysal/graph/tests/test_raster.py'
adding 'libpysal/graph/tests/test_set_ops.py'
adding 'libpysal/graph/tests/test_spatial_lag.py'
adding 'libpysal/graph/tests/test_summary.py'
adding 'libpysal/graph/tests/test_triangulation.py'
adding 'libpysal/graph/tests/test_utils.py'
adding 'libpysal/io/__init__.py'
adding 'libpysal/io/fileio.py'
adding 'libpysal/io/tables.py'
adding 'libpysal/io/geotable/__init__.py'
adding 'libpysal/io/geotable/dbf.py'
adding 'libpysal/io/geotable/file.py'
adding 'libpysal/io/geotable/shp.py'
adding 'libpysal/io/geotable/utils.py'
adding 'libpysal/io/geotable/wrappers.py'
adding 'libpysal/io/geotable/tests/__init__.py'
adding 'libpysal/io/geotable/tests/test_utils.py'
adding 'libpysal/io/iohandlers/__init__.py'
adding 'libpysal/io/iohandlers/arcgis_dbf.py'
adding 'libpysal/io/iohandlers/arcgis_swm.py'
adding 'libpysal/io/iohandlers/arcgis_txt.py'
adding 'libpysal/io/iohandlers/csvWrapper.py'
adding 'libpysal/io/iohandlers/dat.py'
adding 'libpysal/io/iohandlers/db.py'
adding 'libpysal/io/iohandlers/gal.py'
adding 'libpysal/io/iohandlers/geobugs_txt.py'
adding 'libpysal/io/iohandlers/geoda_txt.py'
adding 'libpysal/io/iohandlers/gwt.py'
adding 'libpysal/io/iohandlers/mat.py'
adding 'libpysal/io/iohandlers/mtx.py'
adding 'libpysal/io/iohandlers/pyDbfIO.py'
adding 'libpysal/io/iohandlers/pyShpIO.py'
adding 'libpysal/io/iohandlers/stata_txt.py'
adding 'libpysal/io/iohandlers/template.py'
adding 'libpysal/io/iohandlers/wk1.py'
adding 'libpysal/io/iohandlers/wkt.py'
adding 'libpysal/io/iohandlers/tests/__init__.py'
adding 'libpysal/io/iohandlers/tests/test_arcgis_dbf.py'
adding 'libpysal/io/iohandlers/tests/test_arcgis_swm.py'
adding 'libpysal/io/iohandlers/tests/test_arcgis_txt.py'
adding 'libpysal/io/iohandlers/tests/test_csvWrapper.py'
adding 'libpysal/io/iohandlers/tests/test_dat.py'
adding 'libpysal/io/iohandlers/tests/test_db.py'
adding 'libpysal/io/iohandlers/tests/test_gal.py'
adding 'libpysal/io/iohandlers/tests/test_geobugs_txt.py'
adding 'libpysal/io/iohandlers/tests/test_geoda_txt.py'
adding 'libpysal/io/iohandlers/tests/test_gwt.py'
adding 'libpysal/io/iohandlers/tests/test_mat.py'
adding 'libpysal/io/iohandlers/tests/test_mtx.py'
adding 'libpysal/io/iohandlers/tests/test_pyDbfIO.py'
adding 'libpysal/io/iohandlers/tests/test_pyShpIO.py'
adding 'libpysal/io/iohandlers/tests/test_stata_txt.py'
adding 'libpysal/io/iohandlers/tests/test_wk1.py'
adding 'libpysal/io/iohandlers/tests/test_wkt.py'
adding 'libpysal/io/tests/__init__.py'
adding 'libpysal/io/tests/test_FileIO.py'
adding 'libpysal/io/tests/test_Tables.py'
adding 'libpysal/io/util/__init__.py'
adding 'libpysal/io/util/shapefile.py'
adding 'libpysal/io/util/weight_converter.py'
adding 'libpysal/io/util/wkb.py'
adding 'libpysal/io/util/wkt.py'
adding 'libpysal/io/util/tests/__init__.py'
adding 'libpysal/io/util/tests/test_shapefile.py'
adding 'libpysal/io/util/tests/test_weight_converter.py'
adding 'libpysal/io/util/tests/test_wkt.py'
adding 'libpysal/weights/__init__.py'
adding 'libpysal/weights/_contW_lists.py'
adding 'libpysal/weights/adjtools.py'
adding 'libpysal/weights/contiguity.py'
adding 'libpysal/weights/distance.py'
adding 'libpysal/weights/gabriel.py'
adding 'libpysal/weights/raster.py'
adding 'libpysal/weights/set_operations.py'
adding 'libpysal/weights/spatial_lag.py'
adding 'libpysal/weights/spintW.py'
adding 'libpysal/weights/user.py'
adding 'libpysal/weights/util.py'
adding 'libpysal/weights/weights.py'
adding 'libpysal/weights/tests/__init__.py'
adding 'libpysal/weights/tests/test_Wsets.py'
adding 'libpysal/weights/tests/test__contW_lists.py'
adding 'libpysal/weights/tests/test_adjlist.py'
adding 'libpysal/weights/tests/test_contiguity.py'
adding 'libpysal/weights/tests/test_distance.py'
adding 'libpysal/weights/tests/test_gabriel.py'
adding 'libpysal/weights/tests/test_nx.py'
adding 'libpysal/weights/tests/test_raster.py'
adding 'libpysal/weights/tests/test_spatial_lag.py'
adding 'libpysal/weights/tests/test_spintW.py'
adding 'libpysal/weights/tests/test_user.py'
adding 'libpysal/weights/tests/test_util.py'
adding 'libpysal/weights/tests/test_weights.py'
adding 'libpysal/weights/tests/test_weights_IO.py'
adding 'libpysal-4.12.1.dist-info/licenses/LICENSE.txt'
adding 'libpysal-4.12.1.dist-info/METADATA'
adding 'libpysal-4.12.1.dist-info/WHEEL'
adding 'libpysal-4.12.1.dist-info/top_level.txt'
adding 'libpysal-4.12.1.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built libpysal-4.12.1-py3-none-any.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module
PYTHONPATH=. https_proxy='https://127.0.0.1:9/' no_proxy=localhost python3 -m sphinx -N -d debian/doctrees  -bhtml docs/ debian/html
Running Sphinx v8.2.3
loading translations [en]... done

Extension error!

Versions
========

* Platform:         linux; (Linux-6.12.48+deb13-cloud-amd64-x86_64-with-glibc2.41)
* Python version:   3.13.7 (CPython)
* Sphinx version:   8.2.3
* Docutils version: 0.21.2
* Jinja2 version:   3.1.6
* Pygments version: 2.18.0

Last Messages
=============

None.

Loaded Extensions
=================

None.

Traceback
=========

      File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 544, in load_extension
        raise ExtensionError(
            __('Could not import extension %s') % extname, err
        ) from err
    sphinx.errors.ExtensionError: Could not import extension matplotlib.sphinxext.plot_directive (exception: No module named 'matplotlib')


The full traceback has been saved in:
/tmp/sphinx-err-h7bi4rck.log

To report this error to the developers, please open an issue at <https://github.com/sphinx-doc/sphinx/issues/>. Thanks!
Please also report this if it was a user error, so that a better error message can be provided next time.
make[1]: *** [debian/rules:28: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

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