[From nobody Tue Apr 21 19:21:06 2026 Received: (at maintonly) by bugs.debian.org; 13 Apr 2026 13:05:07 +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, 94; hammy, 150; neutral, 242; 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]:47578) 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 1wCGyR-002lIE-0N for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:05:07 +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=ZoTxwrOGfPlqqSIx3X7gLDbXOu3yT6yzM80ifWIx7I0=; b=SU6Y0pi7tEcZpxZxKRO1IOnP8l qqgfY+HikXhzV8fgnbJwO8SF4bxIhyCTTrFxB2LlxUUgjBlrlxn9TPhct2Fy9IJRPXQLNB6n0/tPx bd7WIGeYrPx+tp51AHuZHa2NC8AM6Tq7+PVjhqdsrEF/iN70vVdFLIX99iXQlTrOZcn2DI1nQoMmA Ei6P2EacyOVTeVsDAy0A4IUwnaKiNsTk3MbCuXRgATmE7TAZ0Q0Ypw0wIbc645tahWddylex0zZpp LoZvcbyCm40AQ08+5tLLIztpXyPWRHYstRW8vCdwLIPvo95fp9wztVL9T2l8+LR+hDiuW6/qnROIM 1bG6hpJg==; 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 1wCGyP-00CJO5-1e for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:05:05 +0000 Date: Mon, 13 Apr 2026 15:05:05 +0200 From: Emanuele Rocca <ema@debian.org> To: maintonly@bugs.debian.org Subject: jellyfish: ftbfs with GCC-16 Message-ID: <adzqAbdYe8QdKE5E@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:jellyfish Version: 2.3.1-5 Severity: important Tags: sid forky ftbfs User: debian-gcc@lists.debian.org Usertags: ftbfs-gcc-16 Hi, jellyfish 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/jellyfish_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. [...] config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor OPTIMIZE="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" LD="aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -lpthread" -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include/jellyfish-2.3.1 -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -lpthread -L/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/lib/aarch64-linux-gnu Warning (mostly harmless): No library found for -ljellyfish-2.0 Generating a Unix-style Makefile Writing Makefile for jellyfish Writing MYMETA.yml and MYMETA.json dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:385: python3.14 setup.py config running config I: pybuild base:385: python3.13 setup.py config running config mv /tmp/m4-ax_python_devel.m4 m4 make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam make[2]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' /usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo /usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i /usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i make all-am make[3]: Entering directory '/build/reproducible-path/jellyfish-2.3.1' g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -std=gnu++11 -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/jellyfish-2.3.1/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish-2.3.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o sub_commands/count_main.o sub_commands/count_main.cc sub_commands/count_main.cc: In instantiation of ‘void mer_counter_base<MerIteratorType, ParserType>::start(int) [with MerIteratorType = mer_qual_iterator; ParserType = sequence_qual_parser]’: sub_commands/count_main.cc:152:16: required from here 152 | virtual void start(int thid) { | ^~~~~ sub_commands/count_main.cc:153:12: error: variable ‘count’ set but not used [-Werror=unused-but-set-variable=] 153 | size_t count = 0; | ^~~~~ sub_commands/count_main.cc: In instantiation of ‘void mer_counter_base<MerIteratorType, ParserType>::start(int) [with MerIteratorType = jellyfish::mer_iterator<jellyfish::mer_overlap_sequence_parser<jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*> > > >, jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0> >; ParserType = jellyfish::mer_overlap_sequence_parser<jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*> > > >]’: sub_commands/count_main.cc:152:16: required from here 152 | virtual void start(int thid) { | ^~~~~ sub_commands/count_main.cc:153:12: error: variable ‘count’ set but not used [-Werror=unused-but-set-variable=] 153 | size_t count = 0; | ^~~~~ cc1plus: all warnings being treated as errors make[3]: *** [Makefile:1705: sub_commands/count_main.o] Error 1 make[3]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' make[2]: *** [Makefile:1040: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' dh_auto_build: error: make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam returned exit code 2 make[1]: *** [debian/rules:70: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/jellyfish-2.3.1' make: *** [debian/rules:22: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 ]