[From nobody Wed Aug 12 08:53:07 2026 Received: (at maintonly) by bugs.debian.org; 13 Apr 2026 13:07:20 +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=-116.6 required=4.0 tests=BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FOURLA,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, 15; hammy, 150; neutral, 199; spammy, 0. spammytokens: 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]:34440) 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 1wCH0a-002lsj-05 for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:07:20 +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-Type:MIME-Version:Message-ID: Subject:To:From:Date:Reply-To:Cc:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=glKFBey7+Har9yih+VBB9UFQIK94FaPaOJ9Kyf5LskQ=; b=USANvJ6Iq2v9n+rAJqWSaob+Qc nt2v6BHvS1mdaMZ5Ch2DH3tccTBD+SrReF2FMRnYYWINcQmByhUYH62s5LALxhu1coR8VL+jcF560 JDcuaguXChD75iAPzLcUyqAwIxu2G6W2kr+f01mX0TcdcSMEDCGYKBFtGG4Hcc5LyVEm2hqKBIR5W t8KVExYrWjyaNLeDAZHsJMG6P2yayjrJGzhU2q2CLZzwAw2X+LUDa7SWFi23sVfb9e11r5yGyAvnv at2RsrH1pQUac7a50WHnlP7i66ar+TDy2GftjFxperYmAx6xpJLtqUaopeTvcGK4DyfIu3WHujcxG P7SNks5g==; 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 1wCH0Y-00CJTV-1L for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:07:18 +0000 Date: Mon, 13 Apr 2026 15:07:18 +0200 From: Emanuele Rocca <ema@debian.org> To: maintonly@bugs.debian.org Subject: mmseqs2: ftbfs with GCC-16 Message-ID: <adzqhjY6wcREQm51@ariel.home> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Debian-User: ema Delivered-To: maintonly@bugs.debian.org Package: src:mmseqs2 Version: 18-8cc5c+ds-1 Severity: important Tags: sid forky ftbfs User: debian-gcc@lists.debian.org Usertags: ftbfs-gcc-16 Hi, mmseqs2 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/mmseqs2_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. [...] 1578: # 1263 "/build/reproducible-path/mmseqs2-18-8cc5c+ds/src/linclust/kmermatcher.cpp" 3 1578: 1 1578: # 1263 "/build/reproducible-path/mmseqs2-18-8cc5c+ds/src/linclust/kmermatcher.cpp" 1578: ); std::cerr.flush(); std::cout.flush(); exit(__status); } while(0); 1578: } 1578: } 1578: 1578: void setKmerLengthAndAlphabet(Parameters &parameters, size_t aaDbSize, int seqTyp) { 1578: if(Parameters::isEqualDbtype(seqTyp, Parameters::DBTYPE_NUCLEOTIDES)){ 1578: if(parameters.kmerSize == 0) { 1578: parameters.kmerSize = std::max(17, static_cast<int>(log(static_cast<float>(aaDbSize))/log(4))); 1578: parameters.spacedKmerPattern = ""; 1578: parameters.alphabetSize = 5; 1578: } 1578: if(parameters.kmersPerSequence == 0){ 1578: parameters.kmersPerSequence = 60; 1578: } 1578: }else{ 1578: if(parameters.kmerSize == 0){ 1578: if((parameters.seqIdThr+0.001)>=0.99){ 1578: parameters.kmerSize = 14; 1578: parameters.alphabetSize = 21; 1578: }else if((parameters.seqIdThr+0.001)>=0.9){ 1578: parameters.kmerSize = 14; 1578: parameters.alphabetSize = 13; 1578: }else{ 1578: parameters.kmerSize = std::max(10, static_cast<int>(log(static_cast<float>(aaDbSize))/log(8.7))); 1578: parameters.alphabetSize = 13; 1578: } 1578: parameters.spacedKmerPattern = ""; 1578: } 1578: if(parameters.kmersPerSequence == 0){ 1578: parameters.kmersPerSequence = 20; 1578: } 1578: } 1578: } 1578: 1578: template std::pair<size_t, size_t> fillKmerPositionArray<0, short>(KmerPosition<short> * kmerArray, size_t kmerArraySize, DBReader<unsigned int> &seqDbr, 1578: Parameters & par, BaseMatrix * subMat, bool hashWholeSequence, size_t hashStartRange, size_t hashEndRange, size_t * hashDistribution); 1578: template std::pair<size_t, size_t> fillKmerPositionArray<1, short>(KmerPosition<short> * kmerArray, size_t kmerArraySize, DBReader<unsigned int> &seqDbr, 1578: Parameters & par, BaseMatrix * subMat, bool hashWholeSequence, size_t hashStartRange, size_t hashEndRange, size_t * hashDistribution); 1578: template std::pair<size_t, size_t> fillKmerPositionArray<2, short>(KmerPosition<short> * kmerArray, size_t kmerArraySize, DBReader<unsigned int> &seqDbr, 1578: Parameters & par, BaseMatrix * subMat, bool hashWholeSequence, size_t hashStartRange, size_t hashEndRange, size_t * hashDistribution); 1578: template std::pair<size_t, size_t> fillKmerPositionArray<0, int>(KmerPosition<int> * kmerArray, size_t kmerArraySize, DBReader<unsigned int> &seqDbr, 1578: Parameters & par, BaseMatrix * subMat, bool hashWholeSequence, size_t hashStartRange, size_t hashEndRange, size_t * hashDistribution); 1578: template std::pair<size_t, size_t> fillKmerPositionArray<1, int>(KmerPosition <int>* kmerArray, size_t kmerArraySize, DBReader<unsigned int> &seqDbr, 1578: Parameters & par, BaseMatrix * subMat, bool hashWholeSequence, size_t hashStartRange, size_t hashEndRange, size_t * hashDistribution); 1578: template std::pair<size_t, size_t> fillKmerPositionArray<2, int>(KmerPosition< int> * kmerArray, size_t kmerArraySize, DBReader<unsigned int> &seqDbr, 1578: Parameters & par, BaseMatrix * subMat, bool hashWholeSequence, size_t hashStartRange, size_t hashEndRange, size_t * hashDistribution); 1578: 1578: template KmerPosition<short> *initKmerPositionMemory(size_t size); 1578: template KmerPosition<int> *initKmerPositionMemory(size_t size); 1578: 1578: template size_t computeMemoryNeededLinearfilter<short>(size_t totalKmer); 1578: template size_t computeMemoryNeededLinearfilter<int>(size_t totalKmer); 1578: 1578: template std::vector<std::pair<size_t, size_t>> setupKmerSplits<short>(Parameters &par, BaseMatrix * subMat, DBReader<unsigned int> &seqDbr, size_t totalKmers, size_t splits); 1578: template std::vector<std::pair<size_t, size_t>> setupKmerSplits<int>(Parameters &par, BaseMatrix * subMat, DBReader<unsigned int> &seqDbr, size_t totalKmers, size_t splits); === END GCC DUMP === make[4]: *** [src/CMakeFiles/mmseqs-framework.dir/build.make:1118: src/CMakeFiles/mmseqs-framework.dir/linclust/kmermatcher.cpp.o] Error 1 make[4]: *** Waiting for unfinished jobs.... make[4]: Leaving directory '/build/reproducible-path/mmseqs2-18-8cc5c+ds/obj-aarch64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:741: src/CMakeFiles/mmseqs-framework.dir/all] Error 2 make[3]: Leaving directory '/build/reproducible-path/mmseqs2-18-8cc5c+ds/obj-aarch64-linux-gnu' make[2]: *** [Makefile:139: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/mmseqs2-18-8cc5c+ds/obj-aarch64-linux-gnu' dh_auto_build: error: cd obj-aarch64-linux-gnu && make -j128 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:41: override_dh_auto_build-arch] Error 25 make[1]: Leaving directory '/build/reproducible-path/mmseqs2-18-8cc5c+ds' make: *** [debian/rules:20: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 ]