Your message dated Sun, 13 Aug 2023 10:50:05 +0000 with message-id <e1qv8fd-000lec...@fasolo.debian.org> and subject line Bug#1037721: fixed in libbpp-seq-omics 2.4.1-10 has caused the Debian Bug report #1037721, regarding libbpp-seq: ftbfs with GCC-13 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.) -- 1037721: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037721 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:libbpp-seq Version: 2.4.1-9 Severity: normal Tags: sid trixie User: debian-...@lists.debian.org Usertags: ftbfs-gcc-13 [This bug is targeted to the upcoming trixie 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-13/g++-13, but succeeds to build with gcc-12/g++-12. The severity of this report will be raised before the trixie release. The full build log can be found at: http://qa-logs.debian.net/2023/05/22/logs/libbpp-seq_2.4.1-9_unstable_gccexp.log The last lines of the build log are at the end of this report. To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html [...] - _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 - _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 - _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 - _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 - _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 - _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 - _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 - _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 - _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 - _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 - _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_@Base 2.4.1 - _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 - _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_@Base 2.4.1 - _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOmEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 - _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 - _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIcSt4pairIKcdESt10_Select1stIS2_ESt4lessIcESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOcEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIcSt4pairIKcdESt10_Select1stIS2_ESt4lessIcESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIcSt4pairIKcdESt10_Select1stIS2_ESt4lessIcESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIdSt4pairIKdmESt10_Select1stIS2_ESt4lessIdESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIdSt4pairIKdmESt10_Select1stIS2_ESt4lessIdESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIdSt4pairIKdmESt10_Select1stIS2_ESt4lessIdESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiSt3mapIidSt4lessIiESaIS0_IS1_dEEEESt10_Select1stIS8_ES4_SaIS8_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiSt3mapIidSt4lessIiESaIS0_IS1_dEEEESt10_Select1stIS8_ES4_SaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOmEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_@Base 2.4.1 _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIcSaIcEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_@Base 2.4.1 _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIdSaIdEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_@Base 2.4.1 _ZSt16__do_uninit_copyIPKN3bpp13BasicSequenceEPS1_ET0_T_S6_S5_@Base 2.4.1 _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElNS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_T1_@Base 2.4.1 - _ZSt19piecewise_construct@Base 2.4.1 +#MISSING: 2.4.1-9# _ZSt19piecewise_construct@Base 2.4.1 + _ZSteqIcSt11char_traitsIcESaIcEEbRKNSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_@Base 2.4.1-9 _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_@Base 2.4.1 _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_OS8_@Base 2.4.1 - _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_@Base 2.4.1 - _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_SA_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_@Base 2.4.1 +#MISSING: 2.4.1-9# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_SA_@Base 2.4.1 _ZTIN3bpp10BowkerTestE@Base 2.4.1 _ZTIN3bpp10IAlignmentE@Base 2.4.1 _ZTIN3bpp10IOSequenceE@Base 2.4.1 @@ -3338,6 +3367,6 @@ _ZTv0_n96_NK3bpp34EchinodermMitochondrialGeneticCode21getNumberOfStopCodonsEv@Base 2.4.1 _ZTv0_n96_NK3bpp34VertebrateMitochondrialGeneticCode21getNumberOfStopCodonsEv@Base 2.4.1 _ZTv0_n96_NK3bpp36InvertebrateMitochondrialGeneticCode21getNumberOfStopCodonsEv@Base 2.4.1 - _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits@Base 2.4.1 +#MISSING: 2.4.1-9# _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits@Base 2.4.1 _ZeqRKN3bpp4SiteES2_@Base 2.4.1 _ZltRKN3bpp4SiteES2_@Base 2.4.1 dh_makeshlibs: error: failing due to earlier errors make: *** [debian/rules:10: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---Source: libbpp-seq-omics Source-Version: 2.4.1-10 Done: Michael R. Crusoe <cru...@debian.org> We believe that the bug you reported is fixed in the latest version of libbpp-seq-omics, 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 1037...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael R. Crusoe <cru...@debian.org> (supplier of updated libbpp-seq-omics 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: Sun, 13 Aug 2023 12:22:12 +0200 Source: libbpp-seq-omics Architecture: source Version: 2.4.1-10 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@debian.org> Closes: 1037718 1037721 1037722 1042137 1042139 1042204 1042230 Changes: libbpp-seq-omics (2.4.1-10) unstable; urgency=medium . * Team upload. * Update symbols file for GCC-13. Closes: #1037718, #1037721, #1037722, #1042137, #1042139, #1042204, #1042230 * Standards-Version: 4.6.2 (routine-update) * d/control: use ${devlibs:Depends} for libbpp-seq-omics-dev Checksums-Sha1: f6c1260262465d2ea13562ab869d8f95bf3262e7 2179 libbpp-seq-omics_2.4.1-10.dsc bf106869f5a386e1f54f3e5b3fc39aebc657a442 17148 libbpp-seq-omics_2.4.1-10.debian.tar.xz 4382be4cde934e22e1dd493acc30c8fef689a0ff 8421 libbpp-seq-omics_2.4.1-10_source.buildinfo Checksums-Sha256: 7a3a3b425467e6b30d705142e63a29a1c91dbe733f052e689966e31f5b6496e8 2179 libbpp-seq-omics_2.4.1-10.dsc 027d003d6b81a1ba63286b62228ed085971f8120ec8ee09a68e425ee8e613092 17148 libbpp-seq-omics_2.4.1-10.debian.tar.xz ff43d9fa26ed044d0b54065e37f58d527b1d0396a6069f49c9017a913e2fc853 8421 libbpp-seq-omics_2.4.1-10_source.buildinfo Files: 226eabee16cb174f91bf8b359e74e774 2179 science optional libbpp-seq-omics_2.4.1-10.dsc 9d6d8fb2fc93519e45c46d0c4c17bc19 17148 science optional libbpp-seq-omics_2.4.1-10.debian.tar.xz 201a84a1846f24a2991d74c75ca80677 8421 science optional libbpp-seq-omics_2.4.1-10_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmTYsBUACgkQPCZ2P2xn 5uIgaBAAgK8hlpkSkB4Ai62HWOEXrMX3HZ3ERHZ2ZC6JHvHHgTOxnG+ShV4i0yWa e58EqHKTfHIMq5R7LbazsNkKoW4lSuqEq76z4alf8mkW/LParEj+1UI0irxrpUre 7/GAd5chvuOp7q2viHKUK3t9TLS6HX4MvSf/aLmQ+j5ozMfDxgOHhaCYTJSzWNNU sqSPnpmk3GITgGEWiBydXhp7nRK6pqlY4yGWCs5dTnn4TRZCjGwGCEt5GHxYHgse 36FAVQrcRhB3Ao+rFpR1x76gHJv75h2r0BkhrAVmZla8Jv0nGRaPxuc94WVrjHuy +hkvv4jTK1yDO9ZuryEUNzppEj2JoUi22AkF7GicKmvt4LM+XA2NENG7GYpXnq1x 4k2/6vkwBZDblhsd5yVkZczfnYA3zF2nNrAVKJ1y8rJX1n06v1koGr7hKgK8yQ6c 4TGWodvDsdPYXNfQV7MkBmsQ/3kkDxQPqFcxWvZ6A22M7rocxSHvS/nDp7L5y7zU JLM06mYLCMEkMt3wPzI8ug5XtRVTT/oNDiVABQ1yFl2/IiI4OEwHQdK3CX4eIuzJ 3hKRQJDKWhGU7x1DoFZ2ZLOEuaqm3+oGFiZCcIxn4RONBTrwy5wOMd9qZH/A7ucH 9oUfFEXi7EaX1l4v0SLvH/dWxAPPISO+HC3zGsnRsZRjYBApD88= =Sag6 -----END PGP SIGNATURE-----
--- End Message ---
