[Debian-med-packaging] Bug#1044608: dipy: Fails to build source after successful build

Sun Aug 13 17:56:52 BST 2023

Source: dipy
Version: 1.7.0-1
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 dipy
> dpkg-buildpackage: info: source version 1.7.0-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Ã‰tienne Mollier <emollier at debian.org>
>  dpkg-source --before-build .
> dpkg-source: info: using options from dipy-1.7.0/debian/source/options: --extend-diff-ignore=(^|/)dipy/COMMIT_INFO.txt$
>  debian/rules clean
> dh clean --buildsystem=pybuild --with python3
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean || true
> I: pybuild base:275: python3.11 setup.py clean 
> /usr/lib/python3/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg`
> !!
> 
>         ********************************************************************************
>         The license_file parameter is deprecated, use license_files instead.
> 
>         By 2023-Oct-30, you need to update your project and remove deprecated calls
>         or your builds will no longer be supported.
> 
>         See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
>         ********************************************************************************
> 
> !!
>   parsed = self.parsers.get(option_name, lambda x: x)(value)
> /usr/lib/python3/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg`
> !!
> 
>         ********************************************************************************
>         The license_file parameter is deprecated, use license_files instead.
> 
>         By 2023-Oct-30, you need to update your project and remove deprecated calls
>         or your builds will no longer be supported.
> 
>         See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
>         ********************************************************************************
> 
> !!
>   parsed = self.parsers.get(option_name, lambda x: x)(value)
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_dipy/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
> rm -rf .pybuild __pycache__
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> : # I: Custom cleaning
> rm -rf build doc-stamp
> /usr/bin/make -C doc clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> rm -rf reference/*.rst
> rm -rf reference_cmd/*.rst
> cd examples_built && rm -rf *.py *.rst *.png fig
> rm -rf _build/*
> rm *-stamp
> rm: cannot remove '*-stamp': No such file or directory
> make[2]: [Makefile:32: clean] Error 1 (ignored)
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> dh_clean
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using options from dipy-1.7.0/debian/source/options: --extend-diff-ignore=(^|/)dipy/COMMIT_INFO.txt$
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building dipy using existing ./dipy_1.7.0.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: file dipy-1.7.0/dipy.egg-info/SOURCES.txt has no final newline (either original or modified version)
> dpkg-source: info: local changes detected, the modified files are:
>  dipy-1.7.0/dipy.egg-info/PKG-INFO
>  dipy-1.7.0/dipy.egg-info/SOURCES.txt
>  dipy-1.7.0/dipy.egg-info/dependency_links.txt
>  dipy-1.7.0/dipy.egg-info/not-zip-safe
>  dipy-1.7.0/dipy.egg-info/requires.txt
>  dipy-1.7.0/dipy.egg-info/top_level.txt
>  dipy-1.7.0/dipy/align/bundlemin.c
>  dipy-1.7.0/dipy/align/crosscorr.c
>  dipy-1.7.0/dipy/align/expectmax.c
>  dipy-1.7.0/dipy/align/parzenhist.c
>  dipy-1.7.0/dipy/align/sumsqdiff.c
>  dipy-1.7.0/dipy/align/transforms.c
>  dipy-1.7.0/dipy/align/vector_fields.c
>  dipy-1.7.0/dipy/core/interpolation.c
>  dipy-1.7.0/dipy/denoise/denspeed.c
>  dipy-1.7.0/dipy/denoise/enhancement_kernel.c
>  dipy-1.7.0/dipy/denoise/nlmeans_block.c
>  dipy-1.7.0/dipy/denoise/pca_noise_estimate.c
>  dipy-1.7.0/dipy/denoise/shift_twist_convolution.c
>  dipy-1.7.0/dipy/direction/bootstrap_direction_getter.c
>  dipy-1.7.0/dipy/direction/closest_peak_direction_getter.c
>  dipy-1.7.0/dipy/direction/pmf.c
>  dipy-1.7.0/dipy/direction/probabilistic_direction_getter.c
>  dipy-1.7.0/dipy/direction/ptt_direction_getter.c
>  dipy-1.7.0/dipy/reconst/benchmarks/bench_csd.py
>  dipy-1.7.0/dipy/reconst/eudx_direction_getter.c
>  dipy-1.7.0/dipy/reconst/quick_squash.c
>  dipy-1.7.0/dipy/reconst/recspeed.c
>  dipy-1.7.0/dipy/reconst/vec_val_sum.c
>  dipy-1.7.0/dipy/segment/clustering_algorithms.c
>  dipy-1.7.0/dipy/segment/clusteringspeed.c
>  dipy-1.7.0/dipy/segment/cythonutils.c
>  dipy-1.7.0/dipy/segment/featurespeed.c
>  dipy-1.7.0/dipy/segment/metricspeed.c
>  dipy-1.7.0/dipy/segment/mrf.c
>  dipy-1.7.0/dipy/tracking/direction_getter.c
>  dipy-1.7.0/dipy/tracking/distances.c
>  dipy-1.7.0/dipy/tracking/fbcmeasures.c
>  dipy-1.7.0/dipy/tracking/localtrack.c
>  dipy-1.7.0/dipy/tracking/propspeed.c
>  dipy-1.7.0/dipy/tracking/stopping_criterion.c
>  dipy-1.7.0/dipy/tracking/streamlinespeed.c
>  dipy-1.7.0/dipy/tracking/vox2track.c
>  dipy-1.7.0/dipy/utils/fast_numpy.c
>  dipy-1.7.0/dipy/utils/omp.c
>  dipy-1.7.0/dipy/workflows/mask.py
>  dipy-1.7.0/dipy/workflows/tests/test_stats.py
>  dipy-1.7.0/dipy/workflows/tracking.py
>  dipy-1.7.0/doc/examples_revamped/01_quick_start/README.rst
>  dipy-1.7.0/doc/examples_revamped/01_quick_start/quick_start.py
>  dipy-1.7.0/doc/examples_revamped/01_quick_start/tracking_introduction_eudx.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/README.rst
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/brain_extraction_dwi.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/denoise_ascm.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/denoise_gibbs.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/denoise_localpca.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/denoise_mppca.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/denoise_nlmeans.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/denoise_patch2self.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/gradients_spheres.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/motion_correction.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/piesno.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/reslice_datasets.py
>  dipy-1.7.0/doc/examples_revamped/04_preprocessing/snr_in_cc.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/README.rst
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/kfold_xval.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_csa.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_csd.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_dki.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_dki_micro.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_dsi.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_dsi_metrics.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_dsid.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_dti.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_forecast.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_fwdti.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_gqi.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_ivim.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_mapmri.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_mcsd.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_msdki.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_qtdmri.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_qti.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_qtiplus.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_rumba.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_sfm.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_sh.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_shore.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/reconst_shore_metrics.py
>  dipy-1.7.0/doc/examples_revamped/07_reconstruction/restore_dti.py
>  dipy-1.7.0/doc/examples_revamped/10_contextual_enhancement/README.rst
>  dipy-1.7.0/doc/examples_revamped/10_contextual_enhancement/contextual_enhancement.py
>  dipy-1.7.0/doc/examples_revamped/10_contextual_enhancement/fiber_to_bundle_coherence.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/README.rst
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/linear_fascicle_evaluation.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/surface_seed.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/tracking_bootstrap_peaks.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/tracking_deterministic.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/tracking_introduction_eudx_1.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/tracking_pft.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/tracking_probabilistic.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/tracking_ptt.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/tracking_rumba.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/tracking_sfm.py
>  dipy-1.7.0/doc/examples_revamped/13_fiber_tracking/tracking_stopping_criterion.py
>  dipy-1.7.0/doc/examples_revamped/17_streamline_analysis/README.rst
>  dipy-1.7.0/doc/examples_revamped/17_streamline_analysis/afq_tract_profiles.py
>  dipy-1.7.0/doc/examples_revamped/17_streamline_analysis/bundle_assignment_maps.py
>  dipy-1.7.0/doc/examples_revamped/17_streamline_analysis/bundle_shape_similarity.py
>  dipy-1.7.0/doc/examples_revamped/17_streamline_analysis/cluster_confidence.py
>  dipy-1.7.0/doc/examples_revamped/17_streamline_analysis/path_length_map.py
>  dipy-1.7.0/doc/examples_revamped/17_streamline_analysis/streamline_length.py
>  dipy-1.7.0/doc/examples_revamped/17_streamline_analysis/streamline_tools.py
>  dipy-1.7.0/doc/examples_revamped/20_registration/README.rst
>  dipy-1.7.0/doc/examples_revamped/20_registration/affine_registration_3d.py
>  dipy-1.7.0/doc/examples_revamped/20_registration/affine_registration_masks.py
>  dipy-1.7.0/doc/examples_revamped/20_registration/bundle_group_registration.py
>  dipy-1.7.0/doc/examples_revamped/20_registration/bundle_registration.py
>  dipy-1.7.0/doc/examples_revamped/20_registration/bundlewarp_registration.py
>  dipy-1.7.0/doc/examples_revamped/20_registration/register_binary_fuzzy.py
>  dipy-1.7.0/doc/examples_revamped/20_registration/streamline_registration.py
>  dipy-1.7.0/doc/examples_revamped/20_registration/syn_registration_2d.py
>  dipy-1.7.0/doc/examples_revamped/20_registration/syn_registration_3d.py
>  dipy-1.7.0/doc/examples_revamped/23_segmentation/README.rst
>  dipy-1.7.0/doc/examples_revamped/23_segmentation/brain_extraction_dwi_1.py
>  dipy-1.7.0/doc/examples_revamped/23_segmentation/bundle_extraction.py
>  dipy-1.7.0/doc/examples_revamped/23_segmentation/fast_streamline_search.py
>  dipy-1.7.0/doc/examples_revamped/23_segmentation/segment_clustering_features.py
>  dipy-1.7.0/doc/examples_revamped/23_segmentation/segment_clustering_metrics.py
>  dipy-1.7.0/doc/examples_revamped/23_segmentation/segment_extending_clustering_framework.py
>  dipy-1.7.0/doc/examples_revamped/23_segmentation/segment_quickbundles.py
>  dipy-1.7.0/doc/examples_revamped/23_segmentation/tissue_classification.py
>  dipy-1.7.0/doc/examples_revamped/26_simulations/README.rst
>  dipy-1.7.0/doc/examples_revamped/26_simulations/reconst_dsid_1.py
>  dipy-1.7.0/doc/examples_revamped/26_simulations/simulate_dki.py
>  dipy-1.7.0/doc/examples_revamped/26_simulations/simulate_multi_tensor.py
>  dipy-1.7.0/doc/examples_revamped/29_Multiprocessing/README.rst
>  dipy-1.7.0/doc/examples_revamped/29_Multiprocessing/reconst_csa_parallel.py
>  dipy-1.7.0/doc/examples_revamped/29_Multiprocessing/reconst_csd_parallel.py
>  dipy-1.7.0/doc/examples_revamped/32_file_formats/README.rst
>  dipy-1.7.0/doc/examples_revamped/32_file_formats/streamline_formats.py
>  dipy-1.7.0/doc/examples_revamped/35_visualization/README.rst
>  dipy-1.7.0/doc/examples_revamped/35_visualization/viz_advanced.py
>  dipy-1.7.0/doc/examples_revamped/35_visualization/viz_bundles.py
>  dipy-1.7.0/doc/examples_revamped/35_visualization/viz_roi_contour.py
>  dipy-1.7.0/doc/examples_revamped/35_visualization/viz_slice.py
>  dipy-1.7.0/doc/examples_revamped/37_workflows/README.rst
>  dipy-1.7.0/doc/examples_revamped/37_workflows/combined_workflow_creation.py
>  dipy-1.7.0/doc/examples_revamped/37_workflows/workflow_creation.py
>  dipy-1.7.0/doc/examples_revamped/README.rst
>  dipy-1.7.0/doc/tools/build_modref_templates.py
>  dipy-1.7.0/doc/tools/docgen_cmd.py
>  dipy-1.7.0/doc/upload_docs.py
>  dipy-1.7.0/setup.py
>  dipy-1.7.0/setup_egg.py
>  dipy-1.7.0/tools/build_dmgs.py
>  dipy-1.7.0/tools/doc_mod.py
>  dipy-1.7.0/tools/doctest_extmods.py
>  dipy-1.7.0/tools/github_stats.py
>  dipy-1.7.0/tools/gitwash_dumper.py
>  dipy-1.7.0/tools/make_examples.py
>  dipy-1.7.0/tools/pack_examples.py
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/dipy_1.7.0-1.diff.kkV8XT
> 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/dipy_1.7.0-1_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.