Your message dated Mon, 04 Jul 2022 13:49:21 +0000 with message-id <e1o8ms1-0006j0...@fasolo.debian.org> and subject line Bug#1012983: fixed in libcifpp 2.0.5-2 has caused the Debian Bug report #1012983, regarding libpdb-redo: ftbfs with GCC-12 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 message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1012983: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1012983 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:libpdb-redo Version: 2.0.3-1 Severity: normal Tags: sid bookworm User: debian-...@lists.debian.org Usertags: ftbfs-gcc-12 [This bug is targeted to the upcoming bookworm release] 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The severity of this report will be raised before the bookworm release. The full build log can be found at: http://qa-logs.debian.net/2022/06/09/gcc12/libpdb-redo_2.0.3-1_unstable_gcc12.log The last lines of the build log are at the end of this report. To build with GCC 11, either set CC=gcc-11 CXX=g++-11 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. apt-get -t=experimental install g++ Common build failures are 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-11/porting_to.html GCC 11 defaults to the GNU++17 standard. If your package installs header files in /usr/include, please don't work around C++17 issues by choosing a lower C++ standard for the package build, but fix these issues to build with the C++17 standard. [...] | ^~~~~~ [ 75%] Building CXX object CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/PRIVATE -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -c /<<PKGBUILDDIR>>/src/Symmetry-2.cpp In file included from /<<PKGBUILDDIR>>/src/DistanceMap.cpp:34: /<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp: At global scope: /<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp:61:50: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations] 61 | class SymmetryAtomIterator : public std::iterator<std::forward_iterator_tag, const mmcif::Atom> | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /usr/include/c++/12/system_error:41, from /usr/include/c++/12/mutex:41, from /<<PKGBUILDDIR>>/src/DistanceMap.cpp:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp:64:30: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | typedef std::iterator<std::forward_iterator_tag, const mmcif::Atom> baseType; | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:79: CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:93: CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o] Error 1 make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:107: CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o] Error 1 In file included from /usr/include/cif++/Structure.hpp:32, from /<<PKGBUILDDIR>>/include/pdb-redo/ClipperWrapper.hpp:29, from /<<PKGBUILDDIR>>/src/Symmetry-2.cpp:33: /usr/include/cif++/Cif++.hpp: In static member function ‘static int cif::detail::ItemReference::item_value_as<char [N]>::compare(const cif::detail::ItemReference&, const char (&)[N], bool)’: /usr/include/cif++/Cif++.hpp:548:81: error: ‘strcmp’ is not a member of ‘std’ 548 | return icase ? cif::icompare(ref.c_str(), value) : std::strcmp(ref.c_str(), value); | ^~~~~~ /usr/include/cif++/Cif++.hpp: In static member function ‘static int cif::detail::ItemReference::item_value_as<const char*>::compare(const cif::detail::ItemReference&, const char*, bool)’: /usr/include/cif++/Cif++.hpp:562:81: error: ‘strcmp’ is not a member of ‘std’ 562 | return icase ? cif::icompare(ref.c_str(), value) : std::strcmp(ref.c_str(), value); | ^~~~~~ /usr/include/cif++/Cif++.hpp: In static member function ‘static int cif::detail::ItemReference::item_value_as<std::__cxx11::basic_string<char> >::compare(const cif::detail::ItemReference&, const std::string&, bool)’: /usr/include/cif++/Cif++.hpp:576:81: error: ‘strcmp’ is not a member of ‘std’ 576 | return icase ? cif::icompare(ref.c_str(), value) : std::strcmp(ref.c_str(), value.c_str()); | ^~~~~~ In file included from /<<PKGBUILDDIR>>/src/Symmetry-2.cpp:34: /<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp: At global scope: /<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp:61:50: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations] 61 | class SymmetryAtomIterator : public std::iterator<std::forward_iterator_tag, const mmcif::Atom> | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /usr/include/c++/12/system_error:41, from /usr/include/c++/12/mutex:41, from /<<PKGBUILDDIR>>/src/Symmetry-2.cpp:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<<PKGBUILDDIR>>/include/pdb-redo/Symmetry-2.hpp:64:30: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | typedef std::iterator<std::forward_iterator_tag, const mmcif::Atom> baseType; | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:177: CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o] Error 1 make[3]: *** [CMakeFiles/pdb-redo.dir/build.make:191: CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o] Error 1 make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:845: CMakeFiles/pdb-redo.dir/all] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[1]: *** [Makefile:149: all] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2 make: *** [debian/rules:11: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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--- Begin Message ---Source: libcifpp Source-Version: 2.0.5-2 Done: Maarten L. Hekkelman <maar...@hekkelman.com> We believe that the bug you reported is fixed in the latest version of libcifpp, 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 1012...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Maarten L. Hekkelman <maar...@hekkelman.com> (supplier of updated libcifpp 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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 04 Jul 2022 15:16:04 +0200 Source: libcifpp Architecture: source Version: 2.0.5-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Maarten L. Hekkelman <maar...@hekkelman.com> Closes: 1012913 1012973 1012983 Changes: libcifpp (2.0.5-2) unstable; urgency=medium . * Include <cstring> to silence g++-12 bug Closes: #1012973, #1012913, #1012973, #1012983 Checksums-Sha1: ee4a7c4bd639d09f42d082a48841374ca179a7f9 2383 libcifpp_2.0.5-2.dsc 5fe93a3617d09e553b644548db3952d110ec66d8 9652 libcifpp_2.0.5-2.debian.tar.xz 29154ca5a3952b92ac70c9052ff0718d255bf9fc 8341 libcifpp_2.0.5-2_amd64.buildinfo Checksums-Sha256: 4acd0232451d1112832f808656cd2943d3084e2c0337e4074b0045c98bd03e85 2383 libcifpp_2.0.5-2.dsc 6dddebfaa4fa2628e27ce9db08b7d5336136b249a59aba6b8779532f7c7e5282 9652 libcifpp_2.0.5-2.debian.tar.xz af335db61853fc772de2859640422158d92f2b233b88e92bc79d1b8c8d2ecc2b 8341 libcifpp_2.0.5-2_amd64.buildinfo Files: 561438093a2131e034b940f1057a5ec4 2383 libs optional libcifpp_2.0.5-2.dsc 54e15cd0304b408bd7c9300956deea9f 9652 libs optional libcifpp_2.0.5-2.debian.tar.xz a163877afd6d3d796371f8cbc8f47420 8341 libs optional libcifpp_2.0.5-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJKBAEBCgA0FiEEpytoJCJrtAfiS56AWHUD7Hrn7c4FAmLC6oYWHG1hYXJ0ZW5A aGVra2VsbWFuLmNvbQAKCRBYdQPseuftzj8VD/45WLzklYXFu/HJn071w320lspW LjcF/M3XYiohzGyqGiFGBygulyKtF0PEqX07lQHuYcRqm6KOHFBb29v4Nz6c9I+Z 7hsmO//aIsI4qWWn1djddAWiHC2Z2oOwnIQ9n0MqD4WNkE3z0bqYA8j+cojD12h2 ccOXXDhBtMgLcwE/CNsYLsQ1pEUnQz9Kb/4TBwUElIuNeFqp3H47Js3LhQqb2wsN LeTU6MqtcI7YcesOllFxSzjWvjIVhBZ/iGRttAf6LoR30PSyx03RpCslPIELBdBy n6MnNoCs2yZh46MlC24EuBVvomWRD7hGHCSt17OCeKi2v9HDFGzUawxOBzemFM2p cvsWNhASawslvpaKw6v638yjlpEIgCqT8A3ay761RX8uoiWlEHL3cAZm4wJyYxS+ N9kq18qV05JyFEdZa0efjky/SkP6Xu0FBL3KU10iEApFNieGk0mmUrcO18DGGMqw e3YjwNEF4qpKM5NkNJ9Lxa2t7QZuQGPXMmwktSc7ZS+/5vR/ubSu1vgQBMpbUZIH P4F1c2jx51oXqvUA+0AENjtHx39Q8hP2mdLEvLn2wytqm7mAwVAA0BdNeVG5XaLi 90ynudPB00PRvy1Oi1NHKyRy0mJJaOJ/u9sRK7KVgHRWyVHnEIsy0qmY8/Ut6d72 VI0PAnYBRAHPFqLHuQ== =vF6P -----END PGP SIGNATURE-----
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