Your message dated Mon, 14 Sep 2026 07:49:17 +0000
with message-id <[email protected]>
and subject line Bug#1133593: fixed in openbabel 3.2.0+dfsg-1
has caused the Debian Bug report #1133593,
regarding openbabel: ftbfs with GCC-16
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1133593: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1133593
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:openbabel
Version: 3.1.1+dfsg-14
Severity: important
Tags: sid forky ftbfs
User: [email protected]
Usertags: ftbfs-gcc-16
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
--- End Message ---
--- Begin Message ---
Source: openbabel
Source-Version: 3.2.0+dfsg-1
Done: Andrius Merkys <[email protected]>
We believe that the bug you reported is fixed in the latest version of
openbabel, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <[email protected]> (supplier of updated openbabel package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 14 Sep 2026 03:20:55 -0400
Source: openbabel
Architecture: source
Version: 3.2.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1133593
Changes:
openbabel (3.2.0+dfsg-1) unstable; urgency=medium
.
* Upload to unstable
* Always skip test/testdistgeom.py in autopkgtest due to timeout and
excessive memory use.
* Use guess-concurrency, limit openmp threads to 1. Thanks Maximiliano Curia
* Get rid of deprecated allocate (removed in c++20). (Closes: #1133593)
Thanks Maximiliano Curia
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