[Debian-med-packaging] Bug#1048586: macsyfinder: Fails to build source after successful build

[Lucas Nussbaum]

Source: macsyfinder
Version: 2.0-2
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 macsyfinder
> dpkg-buildpackage: info: source version 2.0-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh 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 macsyfinder using existing ./macsyfinder_2.0.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: file macsyfinder-2.0/MacSyFinder.egg-info/SOURCES.txt has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/doctrees/developer_guide/api/cluster.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/cluster.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 doc/build/doctrees/developer_guide/api/config.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/config.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 doc/build/doctrees/developer_guide/api/database.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/database.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 doc/build/doctrees/developer_guide/api/definition_parser.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/definition_parser.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 doc/build/doctrees/developer_guide/api/error.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/error.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 doc/build/doctrees/developer_guide/api/gene.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/gene.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 doc/build/doctrees/developer_guide/api/hit.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/hit.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 doc/build/doctrees/developer_guide/api/index.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/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 doc/build/doctrees/developer_guide/api/model.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/model.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 doc/build/doctrees/developer_guide/api/model_conf_parser.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/model_conf_parser.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 doc/build/doctrees/developer_guide/api/package.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/package.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 doc/build/doctrees/developer_guide/api/profile.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/profile.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 doc/build/doctrees/developer_guide/api/registries.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/registries.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 doc/build/doctrees/developer_guide/api/report.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/report.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 doc/build/doctrees/developer_guide/api/scripts.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/scripts.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 doc/build/doctrees/developer_guide/api/search_genes.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/search_genes.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 doc/build/doctrees/developer_guide/api/serialization.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/serialization.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 doc/build/doctrees/developer_guide/api/solution.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/solution.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 doc/build/doctrees/developer_guide/api/system.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/system.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 doc/build/doctrees/developer_guide/api/utils.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/api/utils.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 doc/build/doctrees/developer_guide/index.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/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 doc/build/doctrees/developer_guide/overview.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/developer_guide/overview.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 doc/build/doctrees/environment.pickle: binary file contents changed
> dpkg-source: error: add doc/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 doc/build/doctrees/index.doctree: binary file contents changed
> dpkg-source: error: add doc/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 doc/build/doctrees/modeler_guide/FAQ_modeler.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/modeler_guide/FAQ_modeler.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 doc/build/doctrees/modeler_guide/gallery.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/modeler_guide/gallery.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 doc/build/doctrees/modeler_guide/helper_tools.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/modeler_guide/helper_tools.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 doc/build/doctrees/modeler_guide/index.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/modeler_guide/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 doc/build/doctrees/modeler_guide/modeling.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/modeler_guide/modeling.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 doc/build/doctrees/modeler_guide/models_V1ToV2.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/modeler_guide/models_V1ToV2.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 doc/build/doctrees/modeler_guide/package.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/modeler_guide/package.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 doc/build/doctrees/modeler_guide/publish_package.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/modeler_guide/publish_package.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 doc/build/doctrees/user_guide/FAQ.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/FAQ.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 doc/build/doctrees/user_guide/big_data.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/big_data.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 doc/build/doctrees/user_guide/functioning.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/functioning.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 doc/build/doctrees/user_guide/gembase_convention.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/gembase_convention.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 doc/build/doctrees/user_guide/index.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/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 doc/build/doctrees/user_guide/input.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/input.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 doc/build/doctrees/user_guide/installation.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/installation.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 doc/build/doctrees/user_guide/model_definition.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/model_definition.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 doc/build/doctrees/user_guide/new_v2.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/new_v2.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 doc/build/doctrees/user_guide/outputs.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/outputs.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 doc/build/doctrees/user_guide/quickstart.doctree: binary file contents changed
> dpkg-source: error: add doc/build/doctrees/user_guide/quickstart.doctree in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_downloads/22d0e9e5cd8bcd00d04c2f13cbab13fa/msf_summary.py has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_images/MSF_modelling.svg has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_images/T1SS_example.svg has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_images/gene_obj_interaction.svg has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/_images/graphviz-c80ff5586733885cc13a7fe257e1d17e75060e46.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_images/graphviz-c80ff5586733885cc13a7fe257e1d17e75060e46.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 doc/build/html/_images/inheritance-11adec1aaef2a8b0d5c818e64c87c60bb3ca0bd1.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_images/inheritance-11adec1aaef2a8b0d5c818e64c87c60bb3ca0bd1.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 doc/build/html/_images/inheritance-3ac43d13e597b4b8e29eca3251f6da5f4534de8e.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_images/inheritance-3ac43d13e597b4b8e29eca3251f6da5f4534de8e.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 doc/build/html/_images/inheritance-5996d44049036be8bcaf0de61509c12c1214e265.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_images/inheritance-5996d44049036be8bcaf0de61509c12c1214e265.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 doc/build/html/_images/logo_macsyfinder.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_images/logo_macsyfinder.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 doc/build/html/_images/logo_macsymodels.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_images/logo_macsymodels.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_images/macsyfinder_classes.svg has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/index.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/cluster.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/config.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/database.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/definition_parser.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/error.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/gene.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/hit.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/model.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/model_conf_parser.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/package.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/profile.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/registries.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/report.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/scripts/macsyconfig.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/scripts/macsydata.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/scripts/macsyfinder.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/scripts/macsyprofile.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/search_genes.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/serialization.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/solution.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/system.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_modules/macsypy/utils.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_sources/developer_guide/api/cluster.rst.txt has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_sources/developer_guide/api/hit.rst.txt has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_sources/developer_guide/api/registries.rst.txt has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_sources/developer_guide/index.rst.txt has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_sources/developer_guide/overview.rst.txt has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_sources/user_guide/installation.rst.txt has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/_static/AllFigs.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/AllFigs.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/html/_static/MSF_modelling.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/MSF_modelling.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_static/MSF_modelling.svg has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/_static/T1SS_example.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/T1SS_example.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_static/T1SS_example.svg has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/_static/T3SS_example.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/T3SS_example.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_static/_css/custom.css has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_static/basic.css has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_static/documentation_options.js has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/_static/figure_main-2.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/figure_main-2.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 doc/build/html/_static/file.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/Lato-Bold.ttf: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/Lato-Bold.woff2: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/Lato-BoldItalic.ttf: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/Lato-BoldItalic.woff2: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/Lato-Italic.ttf: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/Lato-Italic.woff2: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/Lato-Regular.ttf: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/Lato-Regular.woff2: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/RobotoSlab-Bold.woff2: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/RobotoSlab-Regular.woff2: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/fontawesome-webfont.eot: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/fontawesome-webfont.ttf: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/fontawesome-webfont.woff: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/fonts/fontawesome-webfont.woff2: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/gene_obj_interaction.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/gene_obj_interaction.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_static/gene_obj_interaction.svg has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/_static/logo_macsyfinder.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/logo_macsyfinder.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 doc/build/html/_static/logo_macsymodels.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/logo_macsymodels.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 doc/build/html/_static/loner.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/loner.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/html/_static/macsyfinder_classes.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/macsyfinder_classes.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_static/macsyfinder_classes.svg has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/_static/minus.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_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 doc/build/html/_static/msf_functionning_step1.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/msf_functionning_step1.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/html/_static/msf_functionning_step2.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/msf_functionning_step2.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/html/_static/msf_functionning_step3.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/msf_functionning_step3.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/html/_static/msf_functionning_step4.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/msf_functionning_step4.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/html/_static/msf_functionning_step5.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/msf_functionning_step5.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_static/msf_summary.py has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/_static/multi_model.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/multi_model.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/html/_static/multi_system.pdf: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/multi_system.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/html/_static/plus.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/plus.png in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/_static/pygments.css has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/_static/spacer.png: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/spacer.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 doc/build/html/_static/under_construction.gif: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/under_construction.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 doc/build/html/_static/under_construction.jpeg: binary file contents changed
> dpkg-source: error: add doc/build/html/_static/under_construction.jpeg in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/cluster.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/config.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/database.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/definition_parser.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/error.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/gene.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/hit.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/index.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/model.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/model_conf_parser.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/package.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/profile.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/registries.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/report.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/scripts.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/search_genes.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/serialization.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/solution.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/system.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/api/utils.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/index.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/developer_guide/overview.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/genindex.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/index.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/modeler_guide/FAQ_modeler.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/modeler_guide/gallery.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/modeler_guide/helper_tools.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/modeler_guide/index.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/modeler_guide/modeling.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/modeler_guide/models_V1ToV2.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/modeler_guide/package.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/modeler_guide/publish_package.html has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/html/objects.inv: binary file contents changed
> dpkg-source: error: add doc/build/html/objects.inv in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/py-modindex.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/search.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/searchindex.js has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/FAQ.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/big_data.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/functioning.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/gembase_convention.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/index.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/input.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/installation.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/model_definition.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/new_v2.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/outputs.html has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/html/user_guide/quickstart.html has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/latex/MSF_modelling.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/MSF_modelling.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/latex/Makefile has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/latex/T1SS_example.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/T1SS_example.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/T3SS_example.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/T3SS_example.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/figure_main-2.png: binary file contents changed
> dpkg-source: error: add doc/build/latex/figure_main-2.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 doc/build/latex/gene_obj_interaction.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/gene_obj_interaction.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/graphviz-c80ff5586733885cc13a7fe257e1d17e75060e46.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/graphviz-c80ff5586733885cc13a7fe257e1d17e75060e46.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/inheritance-1f1a9535b4e521a58745655f7fde6169b803487d.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/inheritance-1f1a9535b4e521a58745655f7fde6169b803487d.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/inheritance-83b34b40613bc1e14b9a1c8cafe3b8f9589da157.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/inheritance-83b34b40613bc1e14b9a1c8cafe3b8f9589da157.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/inheritance-d38d58199ba0af98a545498012fba27f43247208.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/inheritance-d38d58199ba0af98a545498012fba27f43247208.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/latex/latexmkjarc has no final newline (either original or modified version)
> dpkg-source: warning: file macsyfinder-2.0/doc/build/latex/latexmkrc has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/latex/logo_macsyfinder.png: binary file contents changed
> dpkg-source: error: add doc/build/latex/logo_macsyfinder.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 doc/build/latex/logo_macsymodels.png: binary file contents changed
> dpkg-source: error: add doc/build/latex/logo_macsymodels.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 doc/build/latex/loner.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/loner.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/macsyfinder.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/macsyfinder.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/latex/macsyfinder.tex has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/latex/macsyfinder_classes.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/macsyfinder_classes.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/latex/make.bat has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doc/build/latex/msf_functionning_step1.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/msf_functionning_step1.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/msf_functionning_step2.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/msf_functionning_step2.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/msf_functionning_step3.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/msf_functionning_step3.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/msf_functionning_step4.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/msf_functionning_step4.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/msf_functionning_step5.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/msf_functionning_step5.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/multi_model.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/multi_model.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to doc/build/latex/multi_system.pdf: binary file contents changed
> dpkg-source: error: add doc/build/latex/multi_system.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file macsyfinder-2.0/doc/build/latex/sphinxmessages.sty 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/macsyfinder_2.0-2_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.