Package: libbpp-seq
Version: 2.3.1-3
Severity: important
Tags: patch
User: ubuntu-de...@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/
slanga...@ubuntu.com vor...@debian.org
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 \
