[Debichem-devel] Bug#803657: avogadro: FTBFS in experimental: undefined reference to `OpenBabel::OBMol::OBMol(OpenBabel::OBMol const&)'

[Andreas Beckmann]

Source: avogadro
Version: 1.1.1-1~exp3
Severity: serious
Justification: fails to build from source (but built successfully in the past)

avogadro compiles fine in experimental, but fails to link:

[100%] Linking CXX shared module ../../../lib/Avogadro.so
cd /tmp/buildd/avogadro-1.1.1/obj-x86_64-linux-gnu/libavogadro/src/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/python-module.dir/link.txt --verbose=1
/usr/bin/c++  -fPIC -D_FORTIFY_SOURCE=2 -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc  -fPIC -Wl,-z,relro -Wl,-z,defs -Wl,--as-needed -shared -Wl,-soname,Avogadro.so -o ../../../lib/Avogadro.so CMakeFiles/python-module.dir/eigen.cpp.o CMakeFiles/python-module.dir/camera.cpp.o CMakeFiles/python-module.dir/residue.cpp.o CMakeFiles/python-module.dir/primitivelist.cpp.o CMakeFiles/python-module.dir/mesh.cpp.o CMakeFiles/python-module.dir/periodictableview.cpp.o CMakeFiles/python-module.dir/molecule.cpp.o CMakeFiles/python-module.dir/primitive.cpp.o CMakeFiles/python-module.dir/fragment.cpp.o CMakeFiles/python-module.dir/engine.cpp.o CMakeFiles/python-module.dir/atom.cpp.o CMakeFiles/python-module.dir/painter.cpp.o CMakeFiles/python-module.dir/qlist.cpp.o CMakeFiles/python-module.dir/swig.cpp.o CMakeFiles/python-mo
 dule.dir/toolgroup.cpp.o CMakeFiles/python-module.dir/qstring.cpp.o CMakeFiles/python-module.dir/sip.cpp.o CMakeFiles/python-module.dir/moleculefile.cpp.o CMakeFiles/python-module.dir/std_vector.cpp.o CMakeFiles/python-module.dir/moleculelist.cpp.o CMakeFiles/python-module.dir/elementtranslator.cpp.o CMakeFiles/python-module.dir/plugin.cpp.o CMakeFiles/python-module.dir/meshgenerator.cpp.o CMakeFiles/python-module.dir/color.cpp.o CMakeFiles/python-module.dir/glwidget.cpp.o CMakeFiles/python-module.dir/neighborlist.cpp.o CMakeFiles/python-module.dir/cube.cpp.o CMakeFiles/python-module.dir/painterdevice.cpp.o CMakeFiles/python-module.dir/bond.cpp.o CMakeFiles/python-module.dir/pluginmanager.cpp.o CMakeFiles/python-module.dir/animation.cpp.o CMakeFiles/python-module.dir/navigate.cpp.o CMakeFiles/python-module.dir/extension.cpp.o CMakeFiles/python-module.dir/main.cpp.o CMakeFiles/python-module.dir/tool.cpp.o -lstdc++ ../../../lib/libavogadro.so.1.1.1 -lQtOpenGL -lQtGui -lQtCore -lpython
 2.7 -lboost_python -Wl,-rpath,/tmp/buildd/avogadro-1.1.1/obj-x86_64-linux-gnu/lib: 
CMakeFiles/python-module.dir/swig.cpp.o: In function `Molecule_OBMol(Avogadro::Molecule&)':
/tmp/buildd/avogadro-1.1.1/libavogadro/src/python/swig.cpp:554: undefined reference to `OpenBabel::OBMol::OBMol(OpenBabel::OBMol const&)'
/tmp/buildd/avogadro-1.1.1/libavogadro/src/python/swig.cpp:554: undefined reference to `OpenBabel::OBMol::~OBMol()'
/tmp/buildd/avogadro-1.1.1/libavogadro/src/python/swig.cpp:554: undefined reference to `OpenBabel::OBMol::~OBMol()'
collect2: error: ld returned 1 exit status
libavogadro/src/python/CMakeFiles/python-module.dir/build.make:993: recipe for target 'lib/Avogadro.so' failed
make[3]: *** [lib/Avogadro.so] Error 1
make[3]: Leaving directory '/tmp/buildd/avogadro-1.1.1/obj-x86_64-linux-gnu'
CMakeFiles/Makefile2:3089: recipe for target 'libavogadro/src/python/CMakeFiles/python-module.dir/all' failed
make[2]: *** [libavogadro/src/python/CMakeFiles/python-module.dir/all] Error 2
make[2]: Leaving directory '/tmp/buildd/avogadro-1.1.1/obj-x86_64-linux-gnu'
Makefile:152: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/tmp/buildd/avogadro-1.1.1/obj-x86_64-linux-gnu'
dh_auto_build: make -j16 returned exit code 2
debian/rules:20: recipe for target 'build' failed


Andreas