[Debian-med-packaging] Bug#1049071: tombo: Fails to build source after successful build

[Lucas Nussbaum]

Source: tombo
Version: 1.5.1-4
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 tombo
> dpkg-buildpackage: info: source version 1.5.1-4
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --with python3,sphinxdoc --buildsystem=pybuild
>    dh_auto_clean -O--buildsystem=pybuild
> I: pybuild base:275: python3.11 setup.py clean 
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/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 tombo using existing ./tombo_1.5.1.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to docs/build/.doctrees/environment.pickle: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/environment.pickle in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/examples.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/examples.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/filtering.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/filtering.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/index.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/index.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/model_training.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/model_training.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/modified_base_detection.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/modified_base_detection.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/plotting.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/plotting.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/resquiggle.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/resquiggle.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/rna.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/rna.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/text_output.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/text_output.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/tombo.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/tombo.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/.doctrees/tutorials.doctree: binary file contents changed
> dpkg-source: error: add docs/build/.doctrees/tutorials.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/adaptive_forward_pass.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/adaptive_forward_pass.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/adaptive_half_z_scores.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/adaptive_half_z_scores.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/alt_density_est.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/alt_density_est.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/alt_model_comp.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/alt_model_comp.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/begin_forward_pass.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/begin_forward_pass.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/begin_half_z_scores.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/begin_half_z_scores.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/boxplot.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/boxplot.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/dampened_fraction.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/dampened_fraction.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/density.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/density.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/kmer_levels.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/kmer_levels.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/model_comp.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/model_comp.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/old_correction_plot.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/old_correction_plot.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/outlier_robust_llr.gif: binary file contents changed
> dpkg-source: error: add docs/build/_images/outlier_robust_llr.gif in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/per_read_do_novo.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/per_read_do_novo.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/per_read_stat_dist.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/per_read_stat_dist.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/pre_read_5mC.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/pre_read_5mC.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/quantile.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/quantile.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/roc.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/roc.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/sample_comp.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/sample_comp.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/single_samp.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/single_samp.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/stat_dist.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/stat_dist.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/stat_dist_null.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/stat_dist_null.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_images/testing_method_comparison.png: binary file contents changed
> dpkg-source: error: add docs/build/_images/testing_method_comparison.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file tombo-1.5.1/docs/build/_static/basic.css has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/_static/documentation_options.js has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to docs/build/_static/file.png: binary file contents changed
> dpkg-source: error: add docs/build/_static/file.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/Lato-Bold.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Bold.ttf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/Lato-Bold.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Bold.woff2 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/Lato-BoldItalic.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-BoldItalic.ttf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/Lato-BoldItalic.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-BoldItalic.woff2 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/Lato-Italic.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Italic.ttf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/Lato-Italic.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Italic.woff2 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/Lato-Regular.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Regular.ttf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/Lato-Regular.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/Lato-Regular.woff2 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/RobotoSlab-Bold.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/RobotoSlab-Bold.woff2 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/RobotoSlab-Regular.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/RobotoSlab-Regular.woff2 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/fontawesome-webfont.eot: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/fontawesome-webfont.eot in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/fontawesome-webfont.ttf: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/fontawesome-webfont.ttf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/fontawesome-webfont.woff: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/fontawesome-webfont.woff in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/fonts/fontawesome-webfont.woff2: binary file contents changed
> dpkg-source: error: add docs/build/_static/fonts/fontawesome-webfont.woff2 in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/minus.png: binary file contents changed
> dpkg-source: error: add docs/build/_static/minus.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to docs/build/_static/plus.png: binary file contents changed
> dpkg-source: error: add docs/build/_static/plus.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file tombo-1.5.1/docs/build/_static/pygments.css has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/examples.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/filtering.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/genindex.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/index.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/model_training.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/modified_base_detection.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/objects.inv has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/plotting.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/resquiggle.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/rna.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/search.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/searchindex.js has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/text_output.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/tombo.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/docs/build/tutorials.html has no final newline (either original or modified version)
> dpkg-source: warning: file tombo-1.5.1/ont_tombo.egg-info/SOURCES.txt has no final newline (either original or modified version)
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
> 
> 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/tombo_1.5.1-4_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.