Bug#1047210: libbio-scf-perl: Fails to build source after successful build

[Lucas Nussbaum]

Source: libbio-scf-perl
Version: 1.03-6
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 libbio-scf-perl
> dpkg-buildpackage: info: source version 1.03-6
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Jelmer Vernooij <jelmer at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> "/usr/bin/perl" "-MExtUtils::Manifest=fullcheck" -e fullcheck
> rm -f \
>   SCF.bso SCF.def \
>   SCF.exp SCF.x \
>   SCF.bs blib/arch/auto/Bio/SCF/extralibs.all \
>   blib/arch/auto/Bio/SCF/extralibs.ld Makefile.aperl \
>   *.a *.o \
>   *perl.core MYMETA.json \
>   MYMETA.yml SCF.base \
>   SCF.bs SCF.bso \
>   SCF.c SCF.def \
>   SCF.exp SCF.o \
>   SCF_def.old blibdirs.ts \
>   core core.*perl.*.? \
>   core.[0-9] core.[0-9][0-9] \
>   core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \
>   core.[0-9][0-9][0-9][0-9][0-9] libSCF.def \
>   mon.out perl \
>   perl perl.exe \
>   perlmain.c pm_to_blib \
>   pm_to_blib.ts so_locations \
>   tmon.out 
> rm -rf \
>   blib 
> mv Makefile Makefile.old > /dev/null 2>&1
> rm -f \
>   Makefile Makefile.old \
>   SCF.o 
> rm -rf \
>   Bio-SCF-1.03 
> Not in MANIFEST: .pc/.quilt_patches
> Not in MANIFEST: .pc/.quilt_series
> Not in MANIFEST: .pc/.version
> Not in MANIFEST: .pc/0001-Fix-overflowing-casts-from-pointer-to-integer.patch/SCF.xs
> Not in MANIFEST: .pc/applied-patches
> Not in MANIFEST: .pc/spelling.patch/SCF.pm
> Not in MANIFEST: debian/.debhelper/generated/libbio-scf-perl/dh_installchangelogs.dch.trimmed
> Not in MANIFEST: debian/.debhelper/generated/libbio-scf-perl/installed-by-dh_installdocs
> Not in MANIFEST: debian/.debhelper/generated/libbio-scf-perl/installed-by-dh_installexamples
> Not in MANIFEST: debian/.debhelper/generated/libbio-scf-perl/installed-by-dh_installman
> Not in MANIFEST: debian/.debhelper/libbio-scf-perl/dbgsym-build-ids
> Not in MANIFEST: debian/.debhelper/libbio-scf-perl/dbgsym-root/DEBIAN/control
> Not in MANIFEST: debian/.debhelper/libbio-scf-perl/dbgsym-root/DEBIAN/md5sums
> Not in MANIFEST: debian/.debhelper/libbio-scf-perl/dbgsym-root/usr/lib/debug/.build-id/b2/8b55ff26a28ea240e2dc9264706b776ef14e50.debug
> Not in MANIFEST: debian/.debhelper/libbio-scf-perl/dbgsym-root/usr/share/doc/libbio-scf-perl-dbgsym
> Not in MANIFEST: debian/changelog
> Not in MANIFEST: debian/control
> Not in MANIFEST: debian/copyright
> Not in MANIFEST: debian/debhelper-build-stamp
> Not in MANIFEST: debian/files
> Not in MANIFEST: debian/libbio-scf-perl.examples
> Not in MANIFEST: debian/libbio-scf-perl.substvars
> Not in MANIFEST: debian/libbio-scf-perl/DEBIAN/control
> Not in MANIFEST: debian/libbio-scf-perl/DEBIAN/md5sums
> Not in MANIFEST: debian/libbio-scf-perl/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Bio/SCF/SCF.so
> Not in MANIFEST: debian/libbio-scf-perl/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/SCF.pm
> Not in MANIFEST: debian/libbio-scf-perl/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/SCF/Arrays.pm
> Not in MANIFEST: debian/libbio-scf-perl/usr/share/doc/libbio-scf-perl/changelog.Debian.gz
> Not in MANIFEST: debian/libbio-scf-perl/usr/share/doc/libbio-scf-perl/changelog.gz
> Not in MANIFEST: debian/libbio-scf-perl/usr/share/doc/libbio-scf-perl/copyright
> Not in MANIFEST: debian/libbio-scf-perl/usr/share/doc/libbio-scf-perl/examples/read_test_obj.pl
> Not in MANIFEST: debian/libbio-scf-perl/usr/share/doc/libbio-scf-perl/examples/read_test_tied.pl
> Not in MANIFEST: debian/libbio-scf-perl/usr/share/doc/libbio-scf-perl/examples/write_test_obj.pl
> Not in MANIFEST: debian/libbio-scf-perl/usr/share/doc/libbio-scf-perl/examples/write_test_tied.pl
> Not in MANIFEST: debian/libbio-scf-perl/usr/share/man/man3/Bio::SCF.3pm.gz
> Not in MANIFEST: debian/patches/0001-Fix-overflowing-casts-from-pointer-to-integer.patch
> Not in MANIFEST: debian/patches/series
> Not in MANIFEST: debian/patches/spelling.patch
> Not in MANIFEST: debian/rules
> Not in MANIFEST: debian/salsa-ci.yml
> Not in MANIFEST: debian/source/format
> Not in MANIFEST: debian/tests/pkg-perl/smoke-files
> Not in MANIFEST: debian/watch
> Not in MANIFEST: temp.scf
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building libbio-scf-perl using existing ./libbio-scf-perl_1.03.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to temp.scf: binary file contents changed
> dpkg-source: error: add temp.scf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> 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/libbio-scf-perl_1.03-6_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.