[From nobody Wed Apr 22 03:47:05 2026 Received: (at maintonly) by bugs.debian.org; 13 Apr 2026 13:11:20 +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=-116.7 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, 156; hammy, 150; neutral, 181; 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]:41398) 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 1wCH4S-002n38-00 for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:11:20 +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-Transfer-Encoding:Content-Type :MIME-Version:Message-ID:Subject:To:From:Date:Reply-To:Cc:Content-ID: Content-Description:In-Reply-To:References; bh=xP/zqbFY+V49BSVu/cbzCmzUpsPwhcHF2Yba0/QSJtg=; b=fwt9Hh5W/A6gqHDPU1Go1pzkPG iSdX//QOz4hApIuu7j/A92A1QsPVLifB1cABUp+5u4e2N9NymLnDJEx4gIx7k6ZV4bZL2pdFmGy0N VTZ+JMRiZOwl1LMDED2VYxpOnlBsPJYThES9O5ZIMEdbTrd0HGLEyvWIdAm/Ot62VzgtEz2qZ6czq pvwx50YRGdPZ4iWdYe+69QhHQv2U8p9jHgrqaevIBYHY/0YlX6kgr7m3zXHmxTvWPew6Yj47cy+xL 63hsuSelKbXj2WGQL/AJyaoXQu2ASrZ5qqyaNqZGC8kAysio9fHjU+x8NSMRDiVmgoMzQAtAc13o/ nrc5EGdQ==; 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 1wCH4Q-00CJiX-0z for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:11:18 +0000 Date: Mon, 13 Apr 2026 15:11:17 +0200 From: Emanuele Rocca <ema@debian.org> To: maintonly@bugs.debian.org Subject: stacks: ftbfs with GCC-16 Message-ID: <adzrdZo74hMnVYrh@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:stacks Version: 2.68+dfsg-2 Severity: important Tags: sid forky ftbfs User: debian-gcc@lists.debian.org Usertags: ftbfs-gcc-16 Hi, stacks 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/stacks_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. [...] g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/sstacks.o src/sstacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/process_radtags.o src/process_radtags.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/clean.o src/clean.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/file_io.o src/file_io.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/write.o src/write.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/process_shortreads.o src/process_shortreads.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/kmer_filter.o src/kmer_filter.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/clone_filter.o src/clone_filter.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/populations.o src/populations.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/bootstrap.o src/bootstrap.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/export_formats.o src/export_formats.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/mapping_utils.o src/mapping_utils.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/PopSum.o src/PopSum.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/Hwp.o src/Hwp.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/phasedstacks.o src/phasedstacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/tsv2bam.o src/tsv2bam.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/gstacks.o src/gstacks.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/debruijn.o src/debruijn.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o src/SuffixTree.o src/SuffixTree.cc src/MetaPopInfo.cc: In member function ‘void MetaPopInfo::fill_pop_indexes(std::map<int, std::pair<int, int> >&) const’: src/MetaPopInfo.cc:427:30: warning: narrowing conversion of ‘i’ from ‘std::size_t’ {aka ‘long unsigned int’} to ‘int’ [-Wnarrowing] 427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} ); | ^ src/models.cc: In member function ‘double MarukiLowModel::calc_ln_weighted_sum(double, double, double, const LikData&) const’: src/models.cc:736:30: error: ‘numeric_limits’ is not a member of ‘std’ 736 | if (weighted_sum >= std::numeric_limits<double>::min()) { | ^~~~~~~~~~~~~~ src/models.cc:736:45: error: expected primary-expression before ‘double’ 736 | if (weighted_sum >= std::numeric_limits<double>::min()) { | ^~~~~~ src/models.cc:736:45: error: expected ‘)’ before ‘double’ 736 | if (weighted_sum >= std::numeric_limits<double>::min()) { | ~ ^~~~~~ | ) src/models.cc: In member function ‘virtual SiteCall MarukiLowModel::call(const SiteCounts&) const’: src/models.cc:865:31: error: ‘numeric_limits’ is not a member of ‘std’ 865 | double lnl_dimorph = std::numeric_limits<double>::lowest(); | ^~~~~~~~~~~~~~ src/models.cc:865:46: error: expected primary-expression before ‘double’ 865 | double lnl_dimorph = std::numeric_limits<double>::lowest(); | ^~~~~~ In file included from /usr/include/c++/16/cassert:46, from src/constants.h:39, from src/models.h:24, from src/models.cc:30: src/models.cc:883:31: error: ‘numeric_limits’ is not a member of ‘std’ 883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest()); | ^~~~~~~~~~~~~~ src/models.cc:883:46: error: expected primary-expression before ‘double’ 883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest()); | ^~~~~~ src/models.cc:883:46: error: expected ‘)’ before ‘double’ src/models.cc:883:46: error: expected ‘)’ before ‘double’ src/models.cc:883:5: note: to match this ‘(’ 883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest()); | ^~~~~~ src/models.cc: In member function ‘double MarukiLowModel::calc_ln_weighted_sum(double, double, double, const LikData&) const’: src/models.cc:744:1: warning: control reaches end of non-void function [-Wreturn-type] 744 | } | ^ make[3]: *** [Makefile:1121: src/models.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg' make[2]: *** [Makefile:1138: all-recursive] Error 1 make[2]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg' make[1]: *** [Makefile:778: all] Error 2 make[1]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg' dh_auto_build: error: make -j128 returned exit code 2 make: *** [debian/rules:11: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 ]