[From nobody Mon Sep 14 08:51:04 2026 Received: (at maintonly) by bugs.debian.org; 13 Apr 2026 13:09:11 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-116.7 required=4.0 tests=BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER,FVGT_m_MULTI_ODD,HAS_PACKAGE, SPF_HELO_NONE,SPF_NONE,UNPARSEABLE_RELAY,USER_IN_DKIM_WELCOMELIST autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 68; hammy, 150; neutral, 190; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <ema@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:52948) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <ema@debian.org>) id 1wCH2N-002mVx-2P for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:09:11 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Content-Transfer-Encoding:Content-Type :MIME-Version:Message-ID:Subject:To:From:Date:Reply-To:Cc:Content-ID: Content-Description:In-Reply-To:References; bh=mdC16A+UyZ7s/YGkoOGBVzS+hjqFkrMTF8BdkEjiTnc=; b=WSrP9B0Ieymtlx0gHxcXqJkuEl l7VEyUWJ664LwJimyYIu74GQDY6Ctwg6Fm7E6p1p03NyiYHRZVcIJ0vZEGcG8o3ecyf0j/yFaw/D0 tEGub5o2z8NjO9ix1SGv4Fs7p3oUqMdZyD7Yx+O6UF1PvcZPovqaDO6LVUc5RevqYFIzlq1sjxmAD iRZ3AmZlGgiDLWcfOuBKt4Kl6UK0Ev5iy10RBbKzpp7lHLq1sgEt8T1LFotPVRie6sumvgVX9iGft 2DOUe2oxkqG38EDrjG8uyFc1A/MaXb2Mt10Yi9lH9n0MLsyPh8pqLs3VrmY/CJV3cpfqpJz5k36vQ U9zk9/Bg==; Received: from authenticated user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <ema@debian.org>) id 1wCH2M-00CJeK-0J for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:09:10 +0000 Date: Mon, 13 Apr 2026 15:09:09 +0200 From: Emanuele Rocca <ema@debian.org> To: maintonly@bugs.debian.org Subject: openbabel: ftbfs with GCC-16 Message-ID: <adzq9RosbyJU91y5@ariel.home> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-Debian-User: ema Delivered-To: maintonly@bugs.debian.org Package: src:openbabel Version: 3.1.1+dfsg-14 Severity: important Tags: sid forky ftbfs User: debian-gcc@lists.debian.org 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 ]