Hi,
openbabel fails to build in a test rebuild on at least amd64 and arm64 with
gcc-16/g++-16, but builds properly with gcc-15/g++-15. The severity of this
report will be raised before the forky release.
The full build log can be found at:
https://people.debian.org/~ema/gcc-16-rebuilds/output-1/openbabel_arm64.build.xz
The last lines of the build log are at the end of this report.
To build with GCC 16, either set CC=gcc-16 CXX=g++-16 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures include unused (but set) variables, array subscripts
partly outside array bounds, and new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-16/porting_to.html
Please only close this issue after double-checking that the package can be
built correctly with GCC 16.
Please do not reassign this bug to another package. If a fix in another package
is required, then file a bug for the other package (or clone), and mark this
bug as blocked by the bug in the other package.
[...]
from /usr/include/c++/16/bits/stl_algobase.h:70,
from /usr/include/c++/16/bits/specfun.h:44,
from /usr/include/c++/16/cmath:3913,
from /usr/include/c++/16/math.h:36,
from /build/reproducible-path/openbabel-3.1.1+dfsg/include/openbabel/mol.h:41,
from /build/reproducible-path/openbabel-3.1.1+dfsg/include/openbabel/conformersearch.h:24,
from /build/reproducible-path/openbabel-3.1.1+dfsg/src/conformersearch.cpp:20:
/usr/include/c++/16/bits/stl_function.h:134:12: note: declared here
134 | struct binary_function
| ^~~~~~~~~~~~~~~
make[4]: *** [src/CMakeFiles/openbabel.dir/build.make:824: src/CMakeFiles/openbabel.dir/confsearch.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
In file included from /build/reproducible-path/openbabel-3.1.1+dfsg/include/openbabel/format.h:22,
from /build/reproducible-path/openbabel-3.1.1+dfsg/include/openbabel/obconversion.h:37,
from /build/reproducible-path/openbabel-3.1.1+dfsg/src/distgeom.cpp:38:
/build/reproducible-path/openbabel-3.1.1+dfsg/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/16/bits/predefined_ops.h:33,
from /usr/include/c++/16/bits/stl_algobase.h:70,
from /usr/include/c++/16/bits/specfun.h:44,
from /usr/include/c++/16/cmath:3913,
from /usr/include/c++/16/math.h:36,
from /build/reproducible-path/openbabel-3.1.1+dfsg/include/openbabel/mol.h:41,
from /build/reproducible-path/openbabel-3.1.1+dfsg/include/openbabel/distgeom.h:24,
from /build/reproducible-path/openbabel-3.1.1+dfsg/src/distgeom.cpp:22:
/usr/include/c++/16/bits/stl_function.h:134:12: note: declared here
134 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/openbabel-3.1.1+dfsg/src/atom.cpp: In member function ‘unsigned int OpenBabel::OBAtom::GetHyb() const’:
/build/reproducible-path/openbabel-3.1.1+dfsg/src/atom.cpp:495:16: note: non-delegitimized UNSPEC UNSPEC_TLS (98) found in variable location
495 | unsigned int OBAtom::GetHyb() const
| ^~~~~~
/build/reproducible-path/openbabel-3.1.1+dfsg/src/atom.cpp: In member function ‘double OpenBabel::OBAtom::GetPartialCharge()’:
/build/reproducible-path/openbabel-3.1.1+dfsg/src/atom.cpp:531:10: note: non-delegitimized UNSPEC UNSPEC_TLS (98) found in variable location
531 | double OBAtom::GetPartialCharge()
| ^~~~~~
/build/reproducible-path/openbabel-3.1.1+dfsg/src/atom.cpp: In member function ‘bool OpenBabel::OBAtom::IsAromatic() const’:
/build/reproducible-path/openbabel-3.1.1+dfsg/src/atom.cpp:774:8: note: non-delegitimized UNSPEC UNSPEC_TLS (98) found in variable location
774 | bool OBAtom::IsAromatic() const
| ^~~~~~
/build/reproducible-path/openbabel-3.1.1+dfsg/src/atom.cpp: In member function ‘char* OpenBabel::OBAtom::GetType()’:
/build/reproducible-path/openbabel-3.1.1+dfsg/src/atom.cpp:468:9: note: non-delegitimized UNSPEC UNSPEC_TLS (98) found in variable location
468 | char *OBAtom::GetType()
| ^~~~~~
/build/reproducible-path/openbabel-3.1.1+dfsg/src/typer.cpp: In function ‘void __tls_init()’:
/build/reproducible-path/openbabel-3.1.1+dfsg/src/typer.cpp:42:33: note: non-delegitimized UNSPEC UNSPEC_TLS (98) found in variable location
42 | THREAD_LOCAL OBAromaticTyper aromtyper;
| ^~~~~~~~~
/build/reproducible-path/openbabel-3.1.1+dfsg/src/typer.cpp: In member function ‘void OpenBabel::OBAtomTyper::AssignHyb(OpenBabel::OBMol&)’:
/build/reproducible-path/openbabel-3.1.1+dfsg/src/typer.cpp:179:8: note: non-delegitimized UNSPEC UNSPEC_TLS (98) found in variable location
179 | void OBAtomTyper::AssignHyb(OBMol &mol)
| ^~~~~~~~~~~
/build/reproducible-path/openbabel-3.1.1+dfsg/src/mol.cpp: In member function ‘bool OpenBabel::OBMol::CorrectForPH(double)’:
/build/reproducible-path/openbabel-3.1.1+dfsg/src/mol.cpp:2359:8: note: non-delegitimized UNSPEC UNSPEC_TLS (98) found in variable location
2359 | bool OBMol::CorrectForPH(double pH)
| ^~~~~
/build/reproducible-path/openbabel-3.1.1+dfsg/src/mol.cpp: In member function ‘void OpenBabel::OBMol::PerceiveBondOrders()’:
/build/reproducible-path/openbabel-3.1.1+dfsg/src/mol.cpp:3186:8: note: non-delegitimized UNSPEC UNSPEC_TLS (98) found in variable location
3186 | void OBMol::PerceiveBondOrders()
| ^~~~~
make[4]: Leaving directory '/build/reproducible-path/openbabel-3.1.1+dfsg/builddir'
make[3]: *** [CMakeFiles/Makefile2:1722: src/CMakeFiles/openbabel.dir/all] Error 2
make[3]: Leaving directory '/build/reproducible-path/openbabel-3.1.1+dfsg/builddir'
make[2]: *** [Makefile:149: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/openbabel-3.1.1+dfsg/builddir'
dh_auto_build: error: cd builddir && make -j128 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:34: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/openbabel-3.1.1+dfsg'
make: *** [debian/rules:28: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2