[Debian-med-packaging] Bug#906510: tophat: FTBFS in buster/sid (No rule to make target '../src/libtophat.a')

[Santiago Vila]

Package: src:tophat
Version: 2.1.1+dfsg1-1
Severity: serious
Tags: ftbfs

Dear maintainer:

I tried to build this package in buster but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-arch
dh build-arch --no-parallel
   dh_update_autotools_config -a
   dh_autoreconf -a
sh: 1: git: not found
sh: 1: git: not found
sh: 1: git: not found
sh: 1: git: not found
sh: 1: git: not found
configure.ac:20: installing './compile'
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_auto_configure -- --with-boost-libdir=/usr/lib/x86_64-linux-gnu
	./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-boost-libdir=/usr/lib/x86_64-linux-gnu

[... snipped ...]

checking for strdup... yes
checking for strrchr... yes
checking for strtol... yes
checking for strsep... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) none
checking dependency style of g++... (cached) none
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode

-- tophat 2.1.1 Configuration Results --
  C++ compiler:        g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG  -pthread -I/usr/include
  Linker flags:         -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now
  BOOST libraries:     -lboost_thread -lboost_system
  GCC version:         gcc (Debian 8.2.0-3) 8.2.0
  Host System type:    x86_64-pc-linux-gnu
  Install prefix:      /usr
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email bug reports to <tophat.cufflinks at gmail.com>.

make[1]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
   dh_auto_build -a
	make -j1
make[1]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make  all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
Making all in src
make[3]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG  -pthread -I/usr/include -c -o prep_reads.o prep_reads.cpp
make[3]: *** No rule to make target '../src/libtophat.a', needed by 'prep_reads'.  Stop.
make[3]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
make[2]: *** [Makefile:384: all-recursive] Error 1
make[2]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[1]: *** [Makefile:325: all] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_auto_build: make -j1 returned exit code 2
make: *** [debian/rules:14: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------

The build was made with "dpkg-buildpackage -B" in my autobuilder.
Most probably, it also fails here in reproducible builds:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/tophat.html

where you can get a full build log if you need it.

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.

Thanks.