[Debian-astro-maintainers] Bug#1047553: yt: Fails to build source after successful build

[Lucas Nussbaum]

Source: yt
Version: 4.2.1-3
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to build a source package after a successful build
(dpkg-buildpackage ; dpkg-buildpackage -S).

This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.

More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/SourceAfterBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S
> -----------------------------------------------------------------------------------------------------------
> 
> dpkg-buildpackage: info: source package yt
> dpkg-buildpackage: info: source version 4.2.1-3
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Ole Streicher <olebole at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --with python3,numpy3 --buildsystem=pybuild
>    dh_auto_clean -O--buildsystem=pybuild
> I: pybuild base:275: python3.11 setup.py clean 
> Using OpenMP to compile parallel extensions
> /usr/lib/python3/dist-packages/setuptools/config/pyprojecttoml.py:66: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
>   config = read_configuration(filepath, True, ignore_option_errors, dist)
> DefaultPluginManager load plugin answer-testing = yt.utilities.answer_testing.framework:AnswerTesting
> /usr/lib/python3/dist-packages/nose/plugins/manager.py:406: RuntimeWarning: Unable to load plugin answer-testing = yt.utilities.answer_testing.framework:AnswerTesting: The 'ipywidgets>=8.0.0' distribution was not found and is required by the application
>   warn("Unable to load plugin %s: %s" % (ep, e),
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_yt/build' (and everything under it)
> 'build/bdist.linux-x86_64' does not exist -- can't clean it
> 'build/scripts-3.11' does not exist -- can't clean it
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    dh_clean -O--buildsystem=pybuild
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building yt using existing ./yt_4.2.1.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file yt.egg-info/dependency_links.txt, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt.egg-info/not-zip-safe, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt.egg-info/top_level.txt, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt.egg-info/entry_points.txt, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt.egg-info/SOURCES.txt, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt.egg-info/PKG-INFO, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt.egg-info/requires.txt, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/frontends/artio/_artio_caller.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/frontends/artio/artio_headers/LICENSE, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/frontends/ramses/io_utils.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/frontends/gdf/tests/test_outputs.py, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/frontends/gdf/tests/test_outputs_nose.py, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/geometry/oct_container.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/geometry/grid_visitors.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/geometry/oct_visitors.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/geometry/particle_smooth.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/geometry/particle_oct_container.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/geometry/fake_octree.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/geometry/selection_routines.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/geometry/particle_deposit.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/geometry/grid_container.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/cython_fortran_utils.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/ragged_arrays.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/interpolators.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/mesh_utilities.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/bitarray.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/fnv_hash.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/origami.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/line_integral_convolution.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/misc_utilities.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/distance_queue.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/particle_kdtree_tools.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/marching_cubes.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/element_mappings.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/bounded_priority_queue.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/allocation_container.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/geometry_utils.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/amr_kdtools.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/contour_finding.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/mesh_triangulation.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/cosmology_time.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/autogenerated_element_samplers.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/pixelization_routines.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/points_in_volume.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/quad_tree.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/bounding_volume_hierarchy.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/partitioned_grid.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/_octree_raytracing.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/fortran_reader.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/grid_traversal.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/alt_ray_tracers.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/lenses.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/primitives.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/particle_mesh_operations.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/image_samplers.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/cyoctree.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/write_array.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/basic_octree.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/image_utilities.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/depth_first_octree.c, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/cykdtree/kdtree.cpp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file yt/utilities/lib/cykdtree/utils.cpp, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
>  yt-4.2.1/yt/frontends/gamer/cfields.c
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/yt_4.2.1-3.diff.SjOEyX
> dpkg-source: info: Hint: make sure the version in debian/changelog matches the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S' failed to run.


The full build log is available from:
http://qa-logs.debian.net/2023/08/13/yt_4.2.1-3_unstable.log

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.