[Debian-med-packaging] Bug#866069: libbpp-seq installs broken header VectorProbabilisticSiteContainer.h

[Steve Langasek]

Package: libbpp-seq
Version: 2.3.1-3
Severity: important
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu artful ubuntu-patch

Dear maintainers,

The new upstream version of libbpp-seq ships a header,
VectorProbabilisticSiteContainer.h, that is unusable because it references
another header, ../ProbabilisticSite.h, which is not present in the source. 
VectorProbabilisticSiteContainer.h is unused in the package build, so it
doesn't cause any build problems; but it gets included in the package, where
the libbpp-seq-dev postinst bundles it into
/usr/include/Bpp/Seq/Container.all.  This makes Container.all unusable, in
turn causing physamp to FTBFS:

make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 50%] Building CXX object physamp/CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/physamp && /usr/bin/c++    -Wall -Weffc++ -Wshadow -Wconversion   -o CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o -c /<<PKGBUILDDIR>>/physamp/AlignmentOptimizer.cpp
In file included from /usr/include/Bpp/Seq/Container.all:14:0,
                 from /<<PKGBUILDDIR>>/physamp/AlignmentOptimizer.cpp:40:
/usr/include/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h:45:34: fatal error: ../ProbabilisticSite.h: No such file or directory
 #include "../ProbabilisticSite.h"
                                  ^
compilation terminated.
physamp/CMakeFiles/bppalnoptim.dir/build.make:65: recipe for target 'physamp/CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o' failed
make[3]: *** [physamp/CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o] Error 1

I've uploaded the attached patch to Ubuntu to fix this problem by excluding
the broken header from the -dev package.

Please consider applying this patch in Debian as well.

-- 
Steve Langasek                   Give me a lever long enough and a Free OS
Debian Developer                   to set it on, and I can move the world.
Ubuntu Developer                                    http://www.debian.org/
slangasek at ubuntu.com                                     vorlon at debian.org
-------------- next part --------------
diff -Nru libbpp-seq-2.3.1/debian/rules libbpp-seq-2.3.1/debian/rules
--- libbpp-seq-2.3.1/debian/rules	2017-06-22 12:52:59.000000000 -0700
+++ libbpp-seq-2.3.1/debian/rules	2017-06-26 21:00:41.000000000 -0700
@@ -10,6 +10,9 @@
 	dh $@
 
 override_dh_install:
+	# Broken header, don't install (if we do, the postinst will pull it
+	# into generic include files)
+	rm -f debian/tmp/usr/include/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h
 	dh_install
 	d-shlibmove --commit \
 		    --multiarch \