[Debian-med-packaging] Bug#1048643: librostlab-blast: Fails to build source after successful build

[Lucas Nussbaum]

Source: librostlab-blast
Version: 1.0.1-13
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 librostlab-blast
> dpkg-buildpackage: info: source version 1.0.1-13
> 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
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> 	make -j8 distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in lib
> make[3]: Entering directory '/<<PKGBUILDDIR>>/lib'
> test -z "librostlab-blast.la" || rm -f librostlab-blast.la
> rm -rf .libs _libs
> rm -rf blast-parser-parser.cpp blast-parser-parser.output \
> 	rostlab/blast-parser-location.h  rostlab/blast-parser-parser.h  rostlab/blast-parser-position.h  rostlab/blast-parser-stack.h \
> 	stack.hh location.hh position.hh blast-parser-scanner.cpp lex.yy.cc \
> 	librostlab_blast_la-blast-parser-scanner.cpp
> rm -f *.o
> test -z "../doxygen-doc/librostlab-blast.tag -r ../doxygen-doc/html        " || rm -f ../doxygen-doc/librostlab-blast.tag -r ../doxygen-doc/html        
> rm -f *.lo
> rm -f *.tab.c
> test -z "Doxyfile" || rm -f Doxyfile
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./so_locations
> rm -f ./.deps/librostlab_blast_la-blast-parser-driver.Plo
> rm -f ./.deps/librostlab_blast_la-blast-parser-parser.Plo
> rm -f ./.deps/librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.Plo
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib'
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f 
> rm -f config.h stamp-h1
> rm -f libtool config.lt
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> make[3]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f lib/librostlab-blast.tag
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building librostlab-blast using existing ./librostlab-blast_1.0.1.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file config.hin, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file install-sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file aclocal.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file INSTALL, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file ltmain.sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file configure, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file depcomp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file ylwrap, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file missing, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltsugar.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/lt~obsolete.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltversion.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/libtool.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltoptions.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file lib/Makefile.in, use --include-removal to override
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/blast-parser-driver_8h__incl.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/blast-parser-driver_8h__incl.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/blast-parser-driver_8h__incl.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/blast-parser-location_8h__dep__incl.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/blast-parser-location_8h__dep__incl.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/blast-parser-location_8h__dep__incl.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/blast-parser-location_8h__incl.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/blast-parser-location_8h__incl.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/blast-parser-location_8h__incl.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/blast-parser-parser_8h__dep__incl.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/blast-parser-parser_8h__dep__incl.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/blast-parser-parser_8h__dep__incl.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/blast-parser-parser_8h__incl.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/blast-parser-parser_8h__incl.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/blast-parser-parser_8h__incl.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/blast-parser-position_8h__incl.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/blast-parser-position_8h__incl.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/blast-parser-position_8h__incl.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/blast-result_8h__dep__incl.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/blast-result_8h__dep__incl.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/blast-result_8h__dep__incl.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/blast-result_8h__incl.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/blast-result_8h__incl.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/blast-result_8h__incl.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/classrostlab_1_1blast_1_1location__coll__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/classrostlab_1_1blast_1_1location__coll__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/classrostlab_1_1blast_1_1location__coll__graph.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/classrostlab_1_1blast_1_1parser__error__coll__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/classrostlab_1_1blast_1_1parser__error__coll__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/classrostlab_1_1blast_1_1parser__error__coll__graph.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/classrostlab_1_1blast_1_1parser__error__inherit__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/classrostlab_1_1blast_1_1parser__error__inherit__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/classrostlab_1_1blast_1_1parser__error__inherit__graph.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1basic__symbol__coll__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1basic__symbol__coll__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1basic__symbol__coll__graph.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1basic__symbol__inherit__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1basic__symbol__inherit__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1basic__symbol__inherit__graph.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1by__kind__inherit__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1by__kind__inherit__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1by__kind__inherit__graph.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1symbol__type__coll__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1symbol__type__coll__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1symbol__type__coll__graph.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1symbol__type__inherit__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1symbol__type__inherit__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1symbol__type__inherit__graph.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1syntax__error__coll__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1syntax__error__coll__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1syntax__error__coll__graph.pdf in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file librostlab-blast-1.0.1/doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1syntax__error__inherit__graph.md5 has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1syntax__error__inherit__graph.pdf: binary file contents changed
> dpkg-source: error: add doxygen-doc/latex/structrostlab_1_1blast_1_1parser_1_1syntax__error__inherit__graph.pdf 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/librostlab-blast_1.0.1-13_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.