Your message dated Tue, 12 Oct 2021 10:48:42 +0000 with message-id <e1mafks-000b9o...@fasolo.debian.org> and subject line Bug#984092: fixed in libbpp-seq-omics 2.4.1-6 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: 2.4.1-6 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: SHA256 Format: 1.8 Date: Tue, 12 Oct 2021 12:08:43 +0200 Source: libbpp-seq-omics Architecture: source Version: 2.4.1-6 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 (2.4.1-6) unstable; urgency=medium . * Fix watchfile to detect new versions on github * Standards-Version: 4.6.0 (routine-update) * Update symbols file Closes: #984092 * Drop unneeded versioned Depends Checksums-Sha1: c158a66201c2032c84256a8d111eeb18a3628b21 2200 libbpp-seq-omics_2.4.1-6.dsc 3431c271ec2e15e84ced7dad94344a504d9e9acf 17048 libbpp-seq-omics_2.4.1-6.debian.tar.xz 58b292f4eaa05fe2cd007a405188577785bd08e2 7551 libbpp-seq-omics_2.4.1-6_amd64.buildinfo Checksums-Sha256: d9cacb392857e1df5f23a0568e1d3c8baecf25450012e189ecd158f3771296c1 2200 libbpp-seq-omics_2.4.1-6.dsc 1daeab53e91a668c3b1e0eb5113740487f05ab164cd4a2a80703090a6d3b864a 17048 libbpp-seq-omics_2.4.1-6.debian.tar.xz e619692beef3e5083a06f2ca04db79505543b2a7604724acc20098e1611a65fc 7551 libbpp-seq-omics_2.4.1-6_amd64.buildinfo Files: 94add09aed142b5beb9cbe4b9f029db1 2200 science optional libbpp-seq-omics_2.4.1-6.dsc 22da49464da3d3483363572a9d6cc7b3 17048 science optional libbpp-seq-omics_2.4.1-6.debian.tar.xz 07c7cf9c88810bd94f29532563106e71 7551 science optional libbpp-seq-omics_2.4.1-6_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFlYtERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGV0g/+Ph96OaBfCkAgrZAwtr3djIZ5j2pHUAss A7M/K7HsEkWqYBBK2Yb5eHOq07AA/2FMYpVmOU7Fj5wCYUp2lQoucbkJoxpZ/urH EvGTR680U8LGZ+5WIKaZTOlOcYfDOBhjqT5qVLP2Hi7qaIP1Bu/RbT4PjNJ2agWV lKeEnMuY92QDatzhW0GJ2X10V1+GeK+tEW/iLyZTYIEQIBpPPRw7O5dQVW3D9cal 7nPGWNE7X8o2j67V5yRbHdTAikdHdbyLRWp5s6qL0n58JghUBnD3ynlQAHR8RTg3 IslaRswccBoZf+cQQe3ZFqjqDYem3yJ66BTsGhbcYp+ghRnNC3P4RfeS5D3Ujf0y 2QzmqRCF8HNcl07HB9zUwGE2rmXCZLEkPzPYPlASDTnoAsJhkUgrPFxZCz4qq6L6 rS585hy11FW/XuX/gnP7D3ObI4OINkIO8lj7HeTLBqcM+hWniXtEqMzfKj9nv/6P F/pnyZj3yacPF8Boi9RH8NAWaFdyPSmzkGl8gkfW7hm78y/A0WsfM6HXeE8PBQXw mXqH+9jMo2N5F6NOdRRvBv7yMBMb9Gu7YpLS3IADwVbaB/FJYnudJlJ2r8s9GLCU WhiXl8H9Zq+QZLejTEFTZsqXrRSNLTTkHsjjZdfaf09Ar5yM/e6MedztIM+VW/GC E7EmoG2YQjM= =2muZ -----END PGP SIGNATURE-----
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