[Debian-med-packaging] Bug#1048874: hyphy: Fails to build source after successful build

[Lucas Nussbaum]

Source: hyphy
Version: 2.5.51+dfsg-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 hyphy
> dpkg-buildpackage: info: source version 2.5.51+dfsg-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Étienne Mollier <emollier at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --buildsystem=cmake
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean --builddirectory obj-avx
> dh_auto_clean --builddirectory obj-sse3
> dh_auto_clean
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    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 hyphy using existing ./hyphy_2.5.51+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to HYPHYMP: binary file contents changed
> dpkg-source: error: add HYPHYMP in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'HYPHYMP' will not be represented in diff
> dpkg-source: error: cannot represent change to HYPHYMPI: binary file contents changed
> dpkg-source: error: add HYPHYMPI in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'HYPHYMPI' will not be represented in diff
> dpkg-source: error: cannot represent change to hyphy: binary file contents changed
> dpkg-source: error: add hyphy in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'hyphy' will not be represented in diff
> dpkg-source: warning: file hyphy-2.5.51+dfsg/tests/hbltests/data/tempFileTesting-fprintf_fscanf0.4687979362133886 has no final newline (either original or modified version)
> dpkg-source: warning: file hyphy-2.5.51+dfsg/tests/hbltests/data/tempFileTesting-fprintf_fscanf0.8238445035703118 has no final newline (either original or modified version)
> dpkg-source: warning: file hyphy-2.5.51+dfsg/tests/hbltests/data/tempFileTesting-fprintf_fscanf0.9027372938354353 has no final newline (either original or modified version)
> dpkg-source: warning: file hyphy-2.5.51+dfsg/tests/hbltests/data/tempFileTesting-fprintf_fscanf_matrix0.1704761123215957 has no final newline (either original or modified version)
> dpkg-source: warning: file hyphy-2.5.51+dfsg/tests/hbltests/data/tempFileTesting-fprintf_fscanf_matrix0.3165487221713524 has no final newline (either original or modified version)
> dpkg-source: warning: file hyphy-2.5.51+dfsg/tests/hbltests/data/tempFileTesting-fprintf_fscanf_matrix0.440971009535941 has no final newline (either original or modified version)
> dpkg-source: warning: file hyphy-2.5.51+dfsg/tests/hbltests/data/tempFileTesting-fprintf_fscanf_matrix0.5047732006071073 has no final newline (either original or modified version)
> dpkg-source: warning: file hyphy-2.5.51+dfsg/tests/hbltests/data/tempFileTesting-fprintf_fscanf_matrix0.7470210540916354 has no final newline (either original or modified version)
> dpkg-source: warning: file hyphy-2.5.51+dfsg/tests/hbltests/data/tempFileTesting-fprintf_fscanf_matrix0.9913787767270996 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/hyphy_2.5.51+dfsg-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.