Your message dated Tue, 12 Oct 2021 17:03:35 +0000 with message-id <e1malbf-0003kg...@fasolo.debian.org> and subject line Bug#984092: fixed in libbpp-seq-omics 2.4.1-7 has caused the Debian Bug report #984092, regarding libbpp-seq-omics: ftbfs with GCC-11 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.) -- 984092: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984092 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:libbpp-seq-omics Version: 2.4.1-5 Severity: normal Tags: sid bookworm User: debian-...@lists.debian.org Usertags: ftbfs-gcc-11 [This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The severity of this report will be raised before the bookworm release, so nothing has to be done for the bullseye release. The full build log can be found at: http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libbpp-seq-omics_2.4.1-5_unstable_gcc11.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. [...] +++ dpkg-gensymbolsTekV7w 2021-03-01 21:02:24.325500245 +0000 @@ -38,6 +38,7 @@ _ZN3bpp12EdSymbolList25beforeSequenceSubstitutedERKNS_27SymbolListSubstitutionEventE@Base 2.4.1 _ZN3bpp12EdSymbolList7shuffleEv@Base 2.4.1 _ZN3bpp12EdSymbolListixEm@Base 2.4.1 + _ZN3bpp12SequenceMaskC1ERKSt6vectorIbSaIbEEb@Base 2.4.1-5 _ZN3bpp12SequenceMaskD0Ev@Base 2.4.1 _ZN3bpp13AlphabetStateD0Ev@Base 2.4.1 _ZN3bpp13AlphabetStateD1Ev@Base 2.4.1 @@ -126,8 +127,8 @@ _ZN3bpp19OutOfRangeExceptionD2Ev@Base 2.4.1 _ZN3bpp19VectorSiteContainerD0Ev@Base 2.4.1 _ZN3bpp19VectorSiteContainerD1Ev@Base 2.4.1 - _ZN3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE@Base 2.4.1 - _ZN3bpp20AbstractCoreSequence7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 +#MISSING: 2.4.1-5# _ZN3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE@Base 2.4.1 +#MISSING: 2.4.1-5# _ZN3bpp20AbstractCoreSequence7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 _ZN3bpp20BasicSequenceFeature12getAttributeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 _ZN3bpp20BasicSequenceFeature12setAttributeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.1 _ZN3bpp20BasicSequenceFeature13setSequenceIdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 @@ -516,13 +517,17 @@ _ZNSt15_Sp_counted_ptrIDnLN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv@Base 2.4.1 _ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv@Base 2.4.1 _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp10BppNumberIESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_@Base 2.4.1 + _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixEOS5_@Base 2.4.1-5 + _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjSt4lessIS5_ESaISt4pairIKS5_jEEEixERS9_@Base 2.4.1-5 _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base 2.4.1 _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base 2.4.1 _ZNSt5dequeIPN3bpp8MafBlockESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_@Base 2.4.1 _ZNSt5dequeISt6vectorIbSaIbEESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_@Base 2.4.1 _ZNSt5dequeISt6vectorIiSaIiEESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_@Base 2.4.1 - _ZNSt5dequeIjSaIjEE16_M_push_back_auxIJjEEEvDpOT_@Base 2.4.1 - _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_@Base 2.4.1 + _ZNSt5dequeIjSaIjEE12emplace_backIJjEEERjDpOT_@Base 2.4.1-5 +#MISSING: 2.4.1-5# _ZNSt5dequeIjSaIjEE16_M_push_back_auxIJjEEEvDpOT_@Base 2.4.1 + _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEERS5_DpOT_@Base 2.4.1-5 +#MISSING: 2.4.1-5# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_@Base 2.4.1 _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 2.4.1 _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 2.4.1 _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEC1ERKS7_@Base 2.4.1 @@ -557,6 +562,8 @@ _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_@Base 2.4.1 _ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_@Base 2.4.1 _ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_@Base 2.4.1 + _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_@Base 2.4.1-5 + _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_@Base 2.4.1-5 _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev@Base 2.4.1 _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev@Base 2.4.1 _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev@Base 2.4.1 @@ -1150,7 +1157,7 @@ _ZTv0_n56_N3bpp16GtfFeatureReader17getFeaturesOfTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_18SequenceFeatureSetE@Base 2.4.1 _ZTv0_n56_N3bpp17SiteMafStatistics7computeERKNS_8MafBlockE@Base 2.4.1 _ZTv0_n56_N3bpp19AbstractMafIterator20addIterationListenerEPNS_17IterationListenerE@Base 2.4.1 - _ZTv0_n56_N3bpp20AbstractCoreSequence7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 +#MISSING: 2.4.1-5# _ZTv0_n56_N3bpp20AbstractCoreSequence7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 _ZTv0_n56_N3bpp21BedGraphFeatureReader17getFeaturesOfTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_18SequenceFeatureSetE@Base 2.4.1 _ZTv0_n56_N3bpp22SequenceWithAnnotation7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 _ZTv0_n56_N3bpp25PolymorphismMafStatistics7computeERKNS_8MafBlockE@Base 2.4.1 @@ -1175,7 +1182,7 @@ _ZTv0_n64_NK3bpp30SequenceDiversityMafStatistics16getSupportedTagsB5cxx11Ev@Base 2.4.1 _ZTv0_n64_NK3bpp34SiteFrequencySpectrumMafStatistics16getSupportedTagsB5cxx11Ev@Base 2.4.1 _ZTv0_n64_NK3bpp37FourSpeciesPatternCountsMafStatistics16getSupportedTagsB5cxx11Ev@Base 2.4.1 - _ZTv0_n72_N3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE@Base 2.4.1 +#MISSING: 2.4.1-5# _ZTv0_n72_N3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE@Base 2.4.1 _ZTv0_n72_N3bpp22SequenceWithAnnotation10setContentERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE@Base 2.4.1 _ZTv0_n72_N3bpp22SequenceWithAnnotation11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE@Base 2.4.1 _ZTv0_n72_NK3bpp5Fastq12nextSequenceERSiRNS_8SequenceE@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
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--- Begin Message ---Source: libbpp-seq-omics Source-Version: 2.4.1-7 Done: Andreas Tille <ti...@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 984...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@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: Tue, 12 Oct 2021 18:47:10 +0200 Source: libbpp-seq-omics Architecture: source Version: 2.4.1-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Closes: 984092 Changes: libbpp-seq-omics (2.4.1-7) unstable; urgency=medium . * Apply multi-arch hints. + libbpp-seq-omics-dev: Add Multi-Arch: same. * Update symbols file Closes: #984092 Checksums-Sha1: e113670b447dd944a12dafd1f50c537fd2ffc038 2200 libbpp-seq-omics_2.4.1-7.dsc 3e3d99e5e0ff7c4c6afd03a8cd460fbf533931a1 17120 libbpp-seq-omics_2.4.1-7.debian.tar.xz a2a2f3f0219fb2a2fbcf308687a6a05de518a765 7620 libbpp-seq-omics_2.4.1-7_amd64.buildinfo Checksums-Sha256: af47d45a25965c761cd61349bc7139d520036ee4ab194655671eef6d4d2ccada 2200 libbpp-seq-omics_2.4.1-7.dsc 2d4d4b28dadec71b0e0fca2dc89af5509360807273f915236a47c1f7b371d806 17120 libbpp-seq-omics_2.4.1-7.debian.tar.xz 6b9d13d629b9f50dcb625a7cf9dcd1eb922a61ce4979d620686a1f2b0c92993b 7620 libbpp-seq-omics_2.4.1-7_amd64.buildinfo Files: 04524eb507b7d0aba04831883b5e1cc6 2200 science optional libbpp-seq-omics_2.4.1-7.dsc 32591e579b7beeeba9416dd5c9cb1792 17120 science optional libbpp-seq-omics_2.4.1-7.debian.tar.xz fd6f155ac7e9dae6fe407c68a1cbc9f6 7620 science optional libbpp-seq-omics_2.4.1-7_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFlvKwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFcJw//ccdAlXQ36VyqzBVWQbmRwbaEVSbnmMx4 9SlIvL1fuBAsp0PTWU+2EyvKPIuK+X6BPzr+NcL9f7BqB14kD/MoK8EXDiVok11J MFpR0V+xHNVIimHyPrH7NzCdlgf2lV8BompXMeQod3sHpJ2nfG68sn2PGuMKhd3h 2iiF5B1WGe7JdeeYlo7Sgy2I4AgSJ4a9NMRlpIqZi8W8Wng3J7We+ARnMyn1KYIC 88KFMgB5tUjwhrI+ES7PR1PB4paEYVbDSiV8LK4PcWu/eLzakeZWJb8I2tsy7p2m 2ztzbNUXA7JdoWp9xZ7NIoOdYC2OHSNZJpNxTKbCFa+UnaQILA/IwU7bG3M4i03F rgKb796CeIH5rx32NpE0dZkKoYGkCeRPZRV2k9HxzRhgVuMMBuagoNiX1f+fahIM OjLGBo0v1SATg8xR0j3It8KQFx6CO3uLxBLFnwC627Ld+SLmJtKTSXDf+7LXVU9l msSBvmf21tmj0u5zQ+7qdQ9g2aBK96rYjBrkM9nmPYAJsOhH7Pors5meOXOACBJH l8/SGuJsNUbI3zVX3VKwgjsN7NEnywDH8fu6KiTtRkSnFGzqaph6YDc7qCB0gNCR YgdxnoFB1tgagIitr1iLA/D8FANcLYHFt3JsoRPKnEkNX304QBpAXYej/BRyjPY1 UL7JuQb/aio= =IIVP -----END PGP SIGNATURE-----
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