[Debian-med-packaging] Bug#1048497: libslow5lib: Fails to build source after successful build

[Lucas Nussbaum]

Source: libslow5lib
Version: 0.7.0+dfsg-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 libslow5lib
> dpkg-buildpackage: info: source version 0.7.0+dfsg-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 --buildsystem=cmake
>    dh_auto_clean -O--buildsystem=cmake
>    dh_autoreconf_clean -O--buildsystem=cmake
>    dh_clean -O--buildsystem=cmake
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building libslow5lib using existing ./libslow5lib_0.7.0+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of directory lib
> dpkg-source: warning: ignoring deletion of directory include
> dpkg-source: warning: ignoring deletion of directory include/slow5
> dpkg-source: warning: ignoring deletion of file include/slow5/slow5_error.h, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file include/slow5/slow5.h, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file include/slow5/slow5_defs.h, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file include/slow5/slow5_press.h, use --include-removal to override
> dpkg-source: warning: ignoring deletion of directory include/slow5/klib
> dpkg-source: warning: ignoring deletion of file include/slow5/klib/kvec.h, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file include/slow5/klib/khash.h, use --include-removal to override
> dpkg-source: error: cannot represent change to python/__pycache__/test.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add python/__pycache__/test.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/bin/convert_slow5_test: binary file contents changed
> dpkg-source: error: add test/bin/convert_slow5_test in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/convert_slow5_test' will not be represented in diff
> dpkg-source: error: cannot represent change to test/bin/endian_test: binary file contents changed
> dpkg-source: error: add test/bin/endian_test in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/endian_test' will not be represented in diff
> dpkg-source: error: cannot represent change to test/bin/unit_test_ascii: binary file contents changed
> dpkg-source: error: add test/bin/unit_test_ascii in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/unit_test_ascii' will not be represented in diff
> dpkg-source: error: cannot represent change to test/bin/unit_test_binary: binary file contents changed
> dpkg-source: error: add test/bin/unit_test_binary in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/unit_test_binary' will not be represented in diff
> dpkg-source: error: cannot represent change to test/bin/unit_test_empty: binary file contents changed
> dpkg-source: error: add test/bin/unit_test_empty in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/unit_test_empty' will not be represented in diff
> dpkg-source: error: cannot represent change to test/bin/unit_test_enum: binary file contents changed
> dpkg-source: error: add test/bin/unit_test_enum in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/unit_test_enum' will not be represented in diff
> dpkg-source: error: cannot represent change to test/bin/unit_test_helpers: binary file contents changed
> dpkg-source: error: add test/bin/unit_test_helpers in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/unit_test_helpers' will not be represented in diff
> dpkg-source: error: cannot represent change to test/bin/unit_test_lossless: binary file contents changed
> dpkg-source: error: add test/bin/unit_test_lossless in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/unit_test_lossless' will not be represented in diff
> dpkg-source: error: cannot represent change to test/bin/unit_test_press: binary file contents changed
> dpkg-source: error: add test/bin/unit_test_press in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/unit_test_press' will not be represented in diff
> dpkg-source: error: cannot represent change to test/bin/unit_test_two_rg: binary file contents changed
> dpkg-source: error: add test/bin/unit_test_two_rg in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'test/bin/unit_test_two_rg' will not be represented in diff
> 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/libslow5lib_0.7.0+dfsg-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.