[Debichem-devel] Bug#778044: openbabel: ftbfs with GCC-5

[Matthias Klose]

Package: src:openbabel
Version: 2.3.2+dfsg-2
Severity: normal
Tags: sid stretch
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-5

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-5/g++-5, but succeeds to build with gcc-4.9/g++-4.9. The
severity of this report may be raised before the stretch release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc5-20150205/openbabel_2.3.2+dfsg-2_unstable_gcc5.log
The last lines of the build log are at the end of this report.

To build with GCC 5, either set CC=gcc-5 CXX=g++-5 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t experimental install g++ 

Common build failures are C11 as the default C mode, new warnings
resulting in build failures with -Werror turned on, or new/dropped
symbols in Debian symbols files.  For other C/C++ related build failures
see the porting guide at http://gcc.gnu.org/gcc-5/porting_to.html

[...]
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/ichirvr3.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/ichirvr3.c
/usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/openbabel-2.3.2+dfsg/build/CMakeFiles 28
[ 11%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/inchi_dll_main.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/inchi_dll_main.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/inchi_dll_main.c
/usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/openbabel-2.3.2+dfsg/build/CMakeFiles 
[ 11%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiread.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/ichiread.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/ichiread.c
/usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/openbabel-2.3.2+dfsg/build/CMakeFiles 
[ 11%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichimap1.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/ichimap1.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/ichimap1.c
/usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/openbabel-2.3.2+dfsg/build/CMakeFiles 
[ 11%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichinorm.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/ichinorm.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/ichinorm.c
/usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/openbabel-2.3.2+dfsg/build/CMakeFiles 29
[ 12%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_bns.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/ichi_bns.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/ichi_bns.c
/usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/openbabel-2.3.2+dfsg/build/CMakeFiles 
[ 12%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/util.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/util.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/util.c
/usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/openbabel-2.3.2+dfsg/build/CMakeFiles 
[ 12%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichitaut.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/ichitaut.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/ichitaut.c
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[ 13%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiprt1.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/ichiprt1.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/ichiprt1.c
/usr/bin/cmake -E cmake_progress_report /«BUILDDIR»/openbabel-2.3.2+dfsg/build/CMakeFiles 
[ 13%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiisot.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/ichiisot.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/ichiisot.c
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[ 13%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/sha2.o
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cc  -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2  -fopenmp -isystem /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-3.0 -isystem /usr/include/wx-3.0 -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 -I/usr/include/cairo -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include/inchi    -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -fPIC -o CMakeFiles/inchi.dir/sha2.o   -c /«BUILDDIR»/openbabel-2.3.2+dfsg/src/formats/libinchi/sha2.c
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cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cmake -P CMakeFiles/inchi.dir/cmake_clean_target.cmake
cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/src/formats/libinchi && /usr/bin/cmake -E cmake_link_script CMakeFiles/inchi.dir/link.txt --verbose=1
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make[4]: Leaving directory '/«BUILDDIR»/openbabel-2.3.2+dfsg/build'
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dh_auto_build: make -j10 returned exit code 2
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make[1]: Leaving directory '/«BUILDDIR»/openbabel-2.3.2+dfsg'
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