Your message dated Thu, 29 Sep 2022 13:21:01 +0000 with message-id <e1odttj-00f9hz...@fasolo.debian.org> and subject line Bug#1012990: fixed in librostlab-blast 1.0.1-13 has caused the Debian Bug report #1012990, regarding librostlab-blast: 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.) -- 1012990: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1012990 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:librostlab-blast Version: 1.0.1-12 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/librostlab-blast_1.0.1-12_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. [...] | ^~~~~~~~ /usr/include/c++/12/ostream:598:5: note: template argument deduction/substitution failed: /usr/include/rostlab/aux_functions.h:186:43: note: mismatched types ‘const _CharT*’ and ‘rostlab::blast::hit’ 186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; } | ~~~^~~~~~~ /usr/include/c++/12/bits/ostream.tcc:302:5: note: candidate: ‘template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(basic_ostream<_CharT, _Traits>&, const char*)’ 302 | operator<<(basic_ostream<_CharT, _Traits>& __out, const char* __s) | ^~~~~~~~ /usr/include/c++/12/bits/ostream.tcc:302:5: note: template argument deduction/substitution failed: /usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const char*’ 186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; } | ~~~^~~~~~~ /usr/include/c++/12/ostream:615:5: note: candidate: ‘template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(basic_ostream<char, _Traits>&, const char*)’ 615 | operator<<(basic_ostream<char, _Traits>& __out, const char* __s) | ^~~~~~~~ /usr/include/c++/12/ostream:615:5: note: template argument deduction/substitution failed: /usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const char*’ 186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; } | ~~~^~~~~~~ /usr/include/c++/12/ostream:628:5: note: candidate: ‘template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(basic_ostream<char, _Traits>&, const signed char*)’ 628 | operator<<(basic_ostream<char, _Traits>& __out, const signed char* __s) | ^~~~~~~~ /usr/include/c++/12/ostream:628:5: note: template argument deduction/substitution failed: /usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const signed char*’ 186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; } | ~~~^~~~~~~ /usr/include/c++/12/ostream:633:5: note: candidate: ‘template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(basic_ostream<char, _Traits>&, const unsigned char*)’ 633 | operator<<(basic_ostream<char, _Traits>& __out, const unsigned char* __s) | ^~~~~~~~ /usr/include/c++/12/ostream:633:5: note: template argument deduction/substitution failed: /usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const unsigned char*’ 186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; } | ~~~^~~~~~~ /usr/include/c++/12/ostream:754:5: note: candidate: ‘template<class _Ostream, class _Tp> _Ostream&& std::operator<<(_Ostream&&, const _Tp&)’ 754 | operator<<(_Ostream&& __os, const _Tp& __x) | ^~~~~~~~ /usr/include/c++/12/ostream:754:5: note: template argument deduction/substitution failed: /usr/include/c++/12/ostream: In substitution of ‘template<class _Ostream, class _Tp> _Ostream&& std::operator<<(_Ostream&&, const _Tp&) [with _Ostream = std::basic_ostream<char>&; _Tp = rostlab::blast::hit]’: /usr/include/rostlab/aux_functions.h:186:43: required from ‘std::ostream& rostlab::operator<<(std::ostream&, const std::vector<_Tp, _Alloc>&) [with _Tp = blast::hit; _Alloc = std::allocator<blast::hit>; std::ostream = std::basic_ostream<char>]’ ./rostlab/blast-result.h:247:66: required from here /usr/include/c++/12/ostream:754:5: error: no type named ‘type’ in ‘struct std::enable_if<false, void>’ /usr/include/rostlab/aux_functions.h: In instantiation of ‘std::ostream& rostlab::operator<<(std::ostream&, const std::vector<_Tp, _Alloc>&) [with _Tp = blast::hit; _Alloc = std::allocator<blast::hit>; std::ostream = std::basic_ostream<char>]’: ./rostlab/blast-result.h:247:66: required from here rostlab/blast-parser-location.h:158:3: note: candidate: ‘template<class YYChar> std::basic_ostream<YYChar>& rostlab::blast::operator<<(std::basic_ostream<YYChar>&, const position&)’ 158 | operator<< (std::basic_ostream<YYChar>& ostr, const position& pos) | ^~~~~~~~ rostlab/blast-parser-location.h:158:3: note: template argument deduction/substitution failed: /usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const rostlab::blast::position&’ 186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; } | ~~~^~~~~~~ rostlab/blast-parser-location.h:286:3: note: candidate: ‘template<class YYChar> std::basic_ostream<YYChar>& rostlab::blast::operator<<(std::basic_ostream<YYChar>&, const location&)’ 286 | operator<< (std::basic_ostream<YYChar>& ostr, const location& loc) | ^~~~~~~~ rostlab/blast-parser-location.h:286:3: note: template argument deduction/substitution failed: /usr/include/rostlab/aux_functions.h:186:43: note: cannot convert ‘v_i.__gnu_cxx::__normal_iterator<const rostlab::blast::hit*, std::vector<rostlab::blast::hit> >::operator*()’ (type ‘const rostlab::blast::hit’) to type ‘const rostlab::blast::location&’ 186 | { if( v_i != v.begin() ) os << ", "; os << *v_i; } | ~~~^~~~~~~ make[5]: *** [Makefile:575: librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.lo] Error 1 make[5]: Leaving directory '/<<PKGBUILDDIR>>/lib' make[4]: *** [Makefile:445: all] Error 2 make[4]: Leaving directory '/<<PKGBUILDDIR>>/lib' make[3]: *** [Makefile:484: all-recursive] Error 1 make[3]: Leaving directory '/<<PKGBUILDDIR>>' make[2]: *** [Makefile:395: all] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build: error: make -j8 returned exit code 2 make[1]: *** [debian/rules:23: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:8: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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--- Begin Message ---Source: librostlab-blast Source-Version: 1.0.1-13 Done: Étienne Mollier <emoll...@debian.org> We believe that the bug you reported is fixed in the latest version of librostlab-blast, 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. Étienne Mollier <emoll...@debian.org> (supplier of updated librostlab-blast 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: Thu, 29 Sep 2022 14:37:03 +0200 Source: librostlab-blast Architecture: source Version: 1.0.1-13 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll...@debian.org> Closes: 1012990 Changes: librostlab-blast (1.0.1-13) unstable; urgency=medium . * Team upload. * gcc-12.patch: added; fix ftbfs with gcc-12. (Closes: #1012990) * Standards-Version: 4.6.1 (routine-update) * d/rules: filter librostlab-blast.tag to remove build path; attempt to improve build reproducibility. * d/rules: limit dh_installdocs to architecture independent builds. Checksums-Sha1: 69edd53937221bd7accc2149bffbcfd630918289 2522 librostlab-blast_1.0.1-13.dsc 666d475fcd709b263d5a16d8402a51e82b93ad20 6540 librostlab-blast_1.0.1-13.debian.tar.xz Checksums-Sha256: c68f4b941676ed0e46778a5dd0ac260bd3d1c67a9732d9ae6a207ebcb8106822 2522 librostlab-blast_1.0.1-13.dsc 067fb54fe8f18a5ef1d982aca23e52ce4685adf5e4609b8d3f40245a9d13283e 6540 librostlab-blast_1.0.1-13.debian.tar.xz Files: 34887626e8ba7c53a7b5255b2531e428 2522 science optional librostlab-blast_1.0.1-13.dsc 0738f235ddc4811b63d72af1aedfda01 6540 science optional librostlab-blast_1.0.1-13.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmM1lEsUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrfTw/+L0ofcVdgG8KjL7wYmYI3ueT09M5j UGdyw9xvhjJbBOHeUKPzVvSM4HgvCpsgOyLUoZbYFXdP3AADF14awC9ogXkUPIvv W0IetM6Iox+f1yEZIo47/swAFInuioe7l+DWp9f6FUZefz97QJ+W4MPt9sPs/7cR Nx6KPPsu4HPo9IHD+Nfdfzvlduvrkxo6TMgCgq0gAkDKk/lFTt5DnQkooqZaqScq 7CSOIZbCRBmACyk5EYXYNzinaBcJ3XDI14pnZ9A54Dk6p6MLXFaWQp6hu0tcxL2s ZS6y0E46HFWj1sWatimznKmzTbRwoX1b0Z12eO2xHa1jr9Wr+EOpKxPwpw8a6SfT ZlzemzBmG4vdKl0/Zi3VWGADm7s/kv+/Cv6jKIbgxhgDCw3AlroIDeRbLIPxVYqB ZQ7pQHzSK+DG4brMVmF0aCBAf4SoH38csrZG1PEtYURTTk5F6LTSrLWAWLhaBi1y Nl+eCToQKl4+Nh6qhabNXHRjSRMhxK0q+9SnGZ/OwUDm6nro6Y6jFd1OClUr2ke2 JbqhFN4gVNm8amQGim8ySVnUNrlmaY1rPW9g1Fp5Qp8q0Klk02JFAaGxl3ijJZzN wyMBMfnTtna6dSdsRsQbJ+ssvxyKsB8KLoFoKpdtRapEk7L8oj4wmL6gGZBqQdpe H5Yj41R6bRmJfZk= =nTj6 -----END PGP SIGNATURE-----
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