[From nobody Wed Aug 12 14:07:08 2026 Received: (at maintonly) by bugs.debian.org; 13 Apr 2026 13:09:45 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-116.7 required=4.0 tests=BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER,FVGT_m_MULTI_ODD,HAS_PACKAGE, SPF_HELO_NONE,SPF_NONE,UNPARSEABLE_RELAY,USER_IN_DKIM_WELCOMELIST autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 163; hammy, 149; neutral, 158; spammy, 1. spammytokens:0.999-1--curit hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <ema@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:47468) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <ema@debian.org>) id 1wCH2v-002md3-0D for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:09:45 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Content-Transfer-Encoding:Content-Type :MIME-Version:Message-ID:Subject:To:From:Date:Reply-To:Cc:Content-ID: Content-Description:In-Reply-To:References; bh=z5FrU6za5XguNfEcrnP/3y3hKscTeFxtgFZsUALwU+E=; b=YGUiGBRIrjjslQSeeAzk8vI0u3 GrJC6OEF48z9O3f4Jp57McOD1qvwr8ZJFnG06UgVpWaL+jnOY8maxf/Vd6vys5peWguNGEV4J96gm 5GVyAfs/VDbOww9GkhIfT6OBBeVqbjFzDFSZVQjlnqP+WpQp4U4gWPWwCjyYAySXDLrwg/J2fI3mO SbrMjT7QDzOjWbZa2kAUUcC8IMA6LkeEUirDio4o09LecmLKQANyhE0RzzyLGGPvUimi/wS8ywSsx IroVORMKReVcxnSU8oPWVaM1c60wJhr9y0CaxK575Hbp7ffsoizoxxNQSp0lIkUhYg63ETkRTvnMK 9P7Tq6fQ==; Received: from authenticated user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <ema@debian.org>) id 1wCH2t-00CJfL-0v for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:09:43 +0000 Date: Mon, 13 Apr 2026 15:09:42 +0200 From: Emanuele Rocca <ema@debian.org> To: maintonly@bugs.debian.org Subject: pbdagcon: ftbfs with GCC-16 Message-ID: <adzrFjkKhbl2FU0T@ariel.home> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-Debian-User: ema Delivered-To: maintonly@bugs.debian.org Package: src:pbdagcon Version: 0.3+git20180411.c14c422+dfsg-10 Severity: important Tags: sid forky ftbfs User: debian-gcc@lists.debian.org Usertags: ftbfs-gcc-16 Hi, pbdagcon fails to build in a test rebuild on at least amd64 and arm64 with gcc-16/g++-16, but builds properly with gcc-15/g++-15. The severity of this report will be raised before the forky release. The full build log can be found at: https://people.debian.org/~ema/gcc-16-rebuilds/output-1/pbdagcon_arm64.build.xz The last lines of the build log are at the end of this report. To build with GCC 16, either set CC=gcc-16 CXX=g++-16 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. apt-get -t=experimental install g++ Common build failures include unused (but set) variables, array subscripts partly outside array bounds, and new/dropped symbols in Debian symbols files. For other C/C++ related build failures see the porting guide at http://gcc.gnu.org/gcc-16/porting_to.html Please only close this issue after double-checking that the package can be built correctly with GCC 16. Please do not reassign this bug to another package. If a fix in another package is required, then file a bug for the other package (or clone), and mark this bug as blocked by the bug in the other package. [...] 402 | SWAlign(qFragment, tFragment, fragScoreMat, fragPathMat, frontAlignment, | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 403 | scoreFn, EndAnchored); | ~~~~~~~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:41:20: required from ‘int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]’ 41 | return SDPAlign(query, target, scoreFn, wordSize, sdpIns, sdpDel, indelRate, alignment, | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 42 | fragmentSet, prefixFragmentSet, suffixFragmentSet, targetTupleList, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 43 | targetPrefixTupleList, targetSuffixTupleList, maxFragmentChain, alignType, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 44 | detailedAlignment, extendFrontByLocalAlignment, noRecurseUnder, fastSDP, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 45 | minFragmentsToUseGraphPaper); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SimpleAligner.cpp:35:13: required from here 35 | SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize, | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 | config_.sdpIndel, config_.sdpIndel, config_.indelRate*2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | initialAln, Local); | ~~~~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/algorithms/alignment/SWAlignImpl.hpp:135:10: warning: variable ‘matchScorePtr’ set but not used [-Wunused-but-set-variable=] 135 | int *matchScorePtr = &scoreMat[0]; | ^~~~~~~~~~~~~ /usr/include/pbseq/alignment/algorithms/alignment/SWAlignImpl.hpp:136:10: warning: variable ‘gapQScorePtr’ set but not used [-Wunused-but-set-variable=] 136 | int *gapQScorePtr = &scoreMat[1]; | ^~~~~~~~~~~~ /usr/include/pbseq/alignment/algorithms/alignment/SWAlignImpl.hpp:137:10: warning: variable ‘gapTScorePtr’ set but not used [-Wunused-but-set-variable=] 137 | int *gapTScorePtr = &scoreMat[tSeq.length + 1]; | ^~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/tuples/TupleList.hpp:64, from /usr/include/pbseq/alignment/tuples/DNATuple.hpp:13, from /usr/include/pbseq/alignment/tuples/TupleMatching.hpp:5: /usr/include/pbseq/alignment/tuples/TupleListImpl.hpp: In instantiation of ‘void TupleList<T>::FindAll(T&, typename std::vector<T>::const_iterator&, typename std::vector<T>::const_iterator&) [with T = PositionDNATuple; typename std::vector<T>::const_iterator = std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::const_iterator]’: /usr/include/pbseq/alignment/tuples/TupleMatchingImpl.hpp:51:40: required from ‘int StoreMatchingPositions(TSequence&, TupleMetrics&, T_TupleList&, std::vector<CharType>&) [with TSequence = DNASequence; TMatch = Fragment; T_TupleList = TupleList<PositionDNATuple>]’ 51 | targetTupleList.FindAll(queryTuple, curIt, endIt); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:163:27: required from ‘int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>; DNALength = unsigned int]’ 163 | StoreMatchingPositions(qPrefix, tmSmall, targetPrefixTupleList, prefixFragmentSet); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:41:20: required from ‘int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]’ 41 | return SDPAlign(query, target, scoreFn, wordSize, sdpIns, sdpDel, indelRate, alignment, | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 42 | fragmentSet, prefixFragmentSet, suffixFragmentSet, targetTupleList, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 43 | targetPrefixTupleList, targetSuffixTupleList, maxFragmentChain, alignType, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 44 | detailedAlignment, extendFrontByLocalAlignment, noRecurseUnder, fastSDP, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 45 | minFragmentsToUseGraphPaper); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SimpleAligner.cpp:35:13: required from here 35 | SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize, | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 | config_.sdpIndel, config_.sdpIndel, config_.indelRate*2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | initialAln, Local); | ~~~~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/tuples/TupleListImpl.hpp:107:21: error: return type of ‘int PositionDNATuple::operator==(const PositionDNATuple&) const’ is not ‘bool’ 107 | if (*endPos != tuple) { | ~~~~~~~~^~~~~~~~ /usr/include/pbseq/alignment/tuples/TupleListImpl.hpp:107:21: note: used as rewritten candidate for comparison of ‘const PositionDNATuple’ and ‘PositionDNATuple’ make[2]: *** [<builtin>: SimpleAligner.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: Leaving directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' make[1]: *** [makefile:34: cpp] Error 2 make[1]: Leaving directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg' dh_auto_build: error: make -j128 INSTALL="install --strip-program=true" returned exit code 2 make: *** [debian/rules:21: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 ]