Diff of the two buildlogs: -- --- b1/build.log 2024-12-16 23:23:44.775367731 +0000 +++ b2/build.log 2024-12-16 23:31:42.449515186 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 16 10:21:31 -12 2024 -I: pbuilder-time-stamp: 1734387691 +I: Current time: Mon Jan 19 19:46:50 +14 2026 +I: pbuilder-time-stamp: 1768801610 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -46,52 +46,84 @@ dpkg-source: info: applying raw_regex_pattern.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1769919/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3654805/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 19 05:47 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3654805/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3654805/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4a7a6f4992b1479eb551ade742124d76' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1769919' - PS1='# ' - PS2='> ' + INVOCATION_ID=222fd73401a0434a8f3c7835025d8647 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3654805 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sltcHdGq/pbuilderrc_cjHH --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sltcHdGq/b1 --logfile b1/build.log spades_3.15.5+dfsg-8.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sltcHdGq/pbuilderrc_y6N9 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sltcHdGq/b2 --logfile b2/build.log spades_3.15.5+dfsg-8.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1769919/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3654805/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -370,7 +402,7 @@ Get: 195 http://deb.debian.org/debian trixie/main amd64 lynx amd64 2.9.2-1 [641 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 197 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.3.2-5 [216 kB] -Fetched 217 MB in 17s (12.9 MB/s) +Fetched 217 MB in 8s (29.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19965 files and directories currently installed.) @@ -1014,8 +1046,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Dec 16 22:26:01 UTC 2024. -Universal Time is now: Mon Dec 16 22:26:01 UTC 2024. +Local time is now: Mon Jan 19 05:47:48 UTC 2026. +Universal Time is now: Mon Jan 19 05:47:48 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -1195,7 +1227,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/spades-3.15.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spades_3.15.5+dfsg-8_source.changes +I: user script /srv/workspace/pbuilder/3654805/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3654805/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/spades-3.15.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../spades_3.15.5+dfsg-8_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.15.5+dfsg-8 dpkg-buildpackage: info: source distribution unstable @@ -1465,8 +1501,8 @@ CMake that the project does not need compatibility with older versions. --- Configuring done (93.8s) --- Generating done (2.5s) +-- Configuring done (7.8s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -1480,7 +1516,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_auto_build -- all debruijn_test include_test - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1488,92 +1524,188 @@ make[3]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake "--color=" make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake "--color=" +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" +make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/getopt_pp /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake "--color=" -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" +make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend -make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/depend -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" +make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gfa1 /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake "--color=" +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o -MF CMakeFiles/BamTools.dir/BamWriter.cpp.o.d -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamWriter.cpp -[ 0%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/build -[ 0%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -MF CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamMultiReader.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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'/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 0%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -[ 0%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -MF CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o.d -o CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/AffineAlignment.cpp +[ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o +[ 2%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/gqf/CMakeFiles/gqf.dir/gqf.c.o -MF CMakeFiles/gqf.dir/gqf.c.o.d -o CMakeFiles/gqf.dir/gqf.c.o -c 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ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o +[ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong 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ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc && /usr/bin/c++ -DMI_MALLOC_OVERRIDE -DMI_MALLOC_OVERRIDE_GLIBC -DMI_SHOW_ERRORS=1 -DMI_XMALLOC=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/genomic_info.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -MF CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -MF CMakeFiles/llvm-support.dir/Debug.cpp.o.d -o CMakeFiles/llvm-support.dir/Debug.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Debug.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConfig.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamHeader.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o -MF CMakeFiles/BamTools.dir/SamProgram.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgram.cpp +[ 8%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -MF CMakeFiles/ConsensusCore.dir/Sequence.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Sequence.cpp +[ 8%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp +[ 8%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp +[ 8%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/version.dir/cmake_clean_target.cmake /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:610:30: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 610 | printf("%02llx ", j); @@ -1622,114 +1754,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:1615:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1615 | fread(qf->blocks, qf->metadata->size, 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 4%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/CrashRecoveryContext.cpp -[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o -MF CMakeFiles/ConsensusCore.dir/Utils.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Utils.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Utils.cpp -[ 4%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgramChain.cpp -[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o -MF CMakeFiles/ConsensusCore.dir/Version.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Version.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Version.cpp -[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -MF CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Matrix/DenseMatrix.cpp -[ 4%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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+/usr/bin/ranlib libversion.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 8%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 10%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc && /usr/bin/c++ -DMI_MALLOC_OVERRIDE -DMI_MALLOC_OVERRIDE_GLIBC -DMI_SHOW_ERRORS=1 -DMI_XMALLOC=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include 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-I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp -[ 10%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Errno.cpp -[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -[ 11%] Linking CXX static library libedlib.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 -/usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o -/usr/bin/ranlib libedlib.a -[ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -MF CMakeFiles/easel.dir/esl_avx.c.o.d -o CMakeFiles/easel.dir/esl_avx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_avx.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:28: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c: In function 'void _mi_mem_collect(mi_os_tld_t*)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c:466:15: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'mem_region_t' {aka 'struct mem_region_s'} with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess] @@ -1748,7 +1781,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include/mimalloc-types.h:340:8: note: 'mi_heap_t' {aka 'struct mi_heap_s'} declared here 340 | struct mi_heap_s { | ^~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc.c:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:32: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c: At global scope: @@ -1797,6 +1830,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:96:55: note: in expansion of macro 'MI_FORWARD1' 96 | void* operator new[](std::size_t n) noexcept(false) MI_FORWARD1(mi_new,n); | ^~~~~~~~~~~ +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ @@ -1851,8 +1885,10 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:196:53: note: in expansion of macro 'MI_FORWARD2' 196 | void* __libc_realloc(void* p, size_t size) MI_FORWARD2(mi_realloc,p,size); | ^~~~~~~~~~~ -[ 11%] Built target edlib -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend +[ 10%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp +[ 10%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Errno.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:38: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c: In function 'bool _mi_heap_init()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c:192:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'mi_heap_t' {aka 'struct mi_heap_s'} with no trivial copy-assignment [-Wclass-memaccess] @@ -1861,88 +1897,58 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include/mimalloc-types.h:340:8: note: 'mi_heap_t' {aka 'struct mi_heap_s'} declared here 340 | struct mi_heap_s { | ^~~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o +[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp +[ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o +[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -MF CMakeFiles/easel.dir/esl_avx.c.o.d -o CMakeFiles/easel.dir/esl_avx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_avx.c +[ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -MF CMakeFiles/easel.dir/esl_buffer.c.o.d -o CMakeFiles/easel.dir/esl_buffer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_buffer.c -[ 11%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -MF CMakeFiles/binary_io.dir/graph_pack.cpp.o.d -o CMakeFiles/binary_io.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp +[ 11%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Error.cpp +[ 11%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp [ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -MF CMakeFiles/easel.dir/esl_cluster.c.o.d -o CMakeFiles/easel.dir/esl_cluster.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_cluster.c -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 11%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/version.dir/version.cpp.o -MF CMakeFiles/version.dir/version.cpp.o.d -o CMakeFiles/version.dir/version.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/version.cpp -[ 12%] Linking CXX static library libversion.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 -/usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o -/usr/bin/ranlib libversion.a -[ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -MF CMakeFiles/easel.dir/esl_composition.c.o.d -o CMakeFiles/easel.dir/esl_composition.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_composition.c -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Error.cpp -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG 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CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamFile_p.cpp -[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -MF CMakeFiles/easel.dir/esl_distance.c.o.d -o CMakeFiles/easel.dir/esl_distance.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_distance.c -[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -MF CMakeFiles/easel.dir/esl_dmatrix.c.o.d -o CMakeFiles/easel.dir/esl_dmatrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dmatrix.c -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o +[ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o +[ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ByteArray_p.cpp -[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dsqdata.c -[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_exponential.c -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -MF CMakeFiles/easel.dir/esl_fileparser.c.o.d -o CMakeFiles/easel.dir/esl_fileparser.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -MF CMakeFiles/easel.dir/esl_gamma.c.o.d -o CMakeFiles/easel.dir/esl_gamma.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gamma.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] - 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:14: note: did you mean to dereference the pointer? - 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] - 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:10: note: did you mean to dereference the pointer? - 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; - | ^ -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gencode.c -[ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp -[ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_getopts.c +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9, @@ -1952,205 +1958,40 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c -[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gumbel.c -[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp -[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_histogram.c -[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hmm.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] - 325 | if (converged_ && Valley_ > x[2] && x[2] > 2) { - | ^~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 359 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? - | ^~~~~~~ -[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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-DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o 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-/usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o -[ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build -[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -MF CMakeFiles/graphio.dir/gfa_reader.cpp.o.d -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp -[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -MF CMakeFiles/easel.dir/esl_msacluster.c.o.d -o CMakeFiles/easel.dir/esl_msacluster.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msacluster.c -[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -MF CMakeFiles/easel.dir/esl_msafile.c.o.d -o CMakeFiles/easel.dir/esl_msafile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile.c -[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -MF CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d -o CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/FoldingSet.cpp -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -[ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile2.c +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp:1: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 16%] Linking CXX static library libgetopt_pp.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -MF CMakeFiles/easel.dir/esl_msafile_a2m.c.o.d -o CMakeFiles/easel.dir/esl_msafile_a2m.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_a2m.c -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -MF CMakeFiles/easel.dir/esl_msafile_afa.c.o.d -o CMakeFiles/easel.dir/esl_msafile_afa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_afa.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:363:10: warning: unused variable 'loaded' [-Wunused-variable] - 363 | bool loaded = base::BinRead(is, gp); - | ^~~~~~ -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -MF CMakeFiles/easel.dir/esl_msafile_clustal.c.o.d -o CMakeFiles/easel.dir/esl_msafile_clustal.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_clustal.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:207:19: required from here - 207 | graph_io_.Load(basename, g); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::EdgesPositionHandler]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:210:45: required from here - 210 | loader.Load>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] - 101 | bool loaded = io.Load(basename, component); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::EdgeIndex]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:213:34: required from here - 213 | loader.Load>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] - 101 | bool loaded = io.Load(basename, component); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::KmerMapper]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:216:35: required from here - 216 | loader.Load>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] - 101 | bool loaded = io.Load(basename, component); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::FlankingCoverage]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:219:41: required from here - 219 | loader.Load>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] - 101 | bool loaded = io.Load(basename, component); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:253:22: required from here - 253 | graph_io_.BinRead(is, gp.get_mutable()); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::EdgesPositionHandler]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:256:45: required from here - 256 | reader.Read>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] - 130 | auto loaded = io.BinRead(is, component); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::EdgeIndex]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:259:34: required from here - 259 | reader.Read>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] - 130 | auto loaded = io.BinRead(is, component); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:262:35: required from here - 262 | reader.Read>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] - 130 | auto loaded = io.BinRead(is, component); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:265:41: required from here - 265 | reader.Read>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] - 130 | auto loaded = io.BinRead(is, component); - | ^~~~~~ -[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/FormatVariadic.cpp -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_phylip.c -[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Hashing.cpp -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -MF CMakeFiles/easel.dir/esl_msafile_psiblast.c.o.d -o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_psiblast.c -[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Host.cpp -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_selex.c -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -MF CMakeFiles/easel.dir/esl_msafile_stockholm.c.o.d -o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_stockholm.c -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -MF CMakeFiles/easel.dir/esl_msashuffle.c.o.d -o CMakeFiles/easel.dir/esl_msashuffle.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msashuffle.c -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -MF CMakeFiles/easel.dir/esl_msaweight.c.o.d -o CMakeFiles/easel.dir/esl_msaweight.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msaweight.c -[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -MF CMakeFiles/llvm-support.dir/JSON.cpp.o.d -o CMakeFiles/llvm-support.dir/JSON.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/JSON.cpp -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_normal.c -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_paml.c -[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_randomseq.c -[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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-c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_random.c -[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -MF CMakeFiles/easel.dir/esl_ratematrix.c.o.d -o CMakeFiles/easel.dir/esl_ratematrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_ratematrix.c -[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_recorder.c -[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_regexp.c -[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LEB128.cpp -[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_rootfinder.c -[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LineIterator.cpp -[ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -E cmake_link_script CMakeFiles/getopt_pp.dir/link.txt --verbose=1 +[ 16%] Built target gqf +/usr/bin/ar qc libgetopt_pp.a CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o +[ 16%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c +[ 17%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LEB128.cpp +[ 17%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c +/usr/bin/ranlib libgetopt_pp.a In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:73:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2159,59 +2000,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:9: note: in expansion of macro '_bgzf_read' 578 | _bgzf_read(fp->fp, buf, 28); | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here - 46 | void LoadImpl(BinIStream &str, Graph &graph) override { - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sq.c -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio.c -[ 30%] Built target mimalloc-obj -make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/mapping_printer.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Locale.cpp -[ 30%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -MF CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o.d -o CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp:1: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ascii.c -[ 30%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ncbi.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sse.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c:23: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c: In function 'esl_scorematrix_Create': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.h:166:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] - 166 | if ( ((p) = malloc(size)) == NULL) { \ - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c:72:3: note: in expansion of macro 'ESL_ALLOC' - 72 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); - | ^~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.h:23: -/usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here - 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ - | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2227,36 +2015,18 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -MF CMakeFiles/easel.dir/esl_ssi.c.o.d -o CMakeFiles/easel.dir/esl_ssi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_ssi.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 31%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MD5.cpp -[ 31%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined - 5 | safe_mutex_lock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined - 240 | unpackInt16(const uint8_t* buffer); - | ^~~~~~~~~~~ -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stack.c -[ 32%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o +[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c -[ 32%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c +[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); @@ -2268,27 +2038,25 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stats.c -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stopwatch.c -[ 32%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 18%] Built target getopt_pp +[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c +[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c -[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp -[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stretchexp.c +[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:344:62: warning: format '%lld' expects argument of type 'long long int', but argument 8 has type 'int64_t' {aka 'long int'} [-Wformat=] 344 | fprintf(fp, "mem=%d head=%d tail=%d n=%d length=%d id=%lld ordered=%d num_adders=%d num_getters=%d\n", @@ -2308,27 +2076,19 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ -[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -MF CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d -o CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MemAlloc.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:97:9: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' - 97 | DeleteLink(w, e2); - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:109:33: required from here - 109 | helper.LinkEdges(e1, e2); - | ~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:102:14: warning: unused variable 'res' [-Wunused-variable] - 102 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); - | ^~~ -[ 34%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_tree.c -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vectorops.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_threads.c +[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined + 5 | safe_mutex_lock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined + 240 | unpackInt16(const uint8_t* buffer); + | ^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); @@ -2340,14 +2100,18 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -MF CMakeFiles/easel.dir/esl_vmx.c.o.d -o CMakeFiles/easel.dir/esl_vmx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vmx.c -[ 34%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c -[ 36%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o +[ 19%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c -[ 36%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o +[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o +[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -MF CMakeFiles/easel.dir/esl_distance.c.o.d -o CMakeFiles/easel.dir/esl_distance.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_distance.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp +[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp +[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined @@ -2360,39 +2124,263 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.c -[ 37%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_workqueue.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_wuss.c -[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] + 325 | if (converged_ && Valley_ > x[2] && x[2] > 2) { + | ^~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 359 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? + | ^~~~~~~ +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -MF CMakeFiles/easel.dir/esl_dmatrix.c.o.d -o CMakeFiles/easel.dir/esl_dmatrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dmatrix.c +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dsqdata.c +[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o +[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LineIterator.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Locale.cpp +[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MD5.cpp +[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:363:10: warning: unused variable 'loaded' [-Wunused-variable] + 363 | bool loaded = base::BinRead(is, gp); + | ^~~~~~ +[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -MF CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d -o CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MemAlloc.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp:1: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_exponential.c +[ 20%] Linking C static library libgfa1.a +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:207:19: required from here + 207 | graph_io_.Load(basename, g); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +[ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::EdgesPositionHandler]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:210:45: required from here + 210 | loader.Load>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] + 101 | bool loaded = io.Load(basename, component); + | ^~~~~~ +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::EdgeIndex]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:213:34: required from here + 213 | loader.Load>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] + 101 | bool loaded = io.Load(basename, component); + | ^~~~~~ +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -MF CMakeFiles/easel.dir/esl_fileparser.c.o.d -o CMakeFiles/easel.dir/esl_fileparser.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::KmerMapper]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:216:35: required from here + 216 | loader.Load>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] + 101 | bool loaded = io.Load(basename, component); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::FlankingCoverage]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:219:41: required from here + 219 | loader.Load>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] + 101 | bool loaded = io.Load(basename, component); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:253:22: required from here + 253 | graph_io_.BinRead(is, gp.get_mutable()); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::EdgesPositionHandler]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:256:45: required from here + 256 | reader.Read>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] + 130 | auto loaded = io.BinRead(is, component); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::EdgeIndex]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:259:34: required from here + 259 | reader.Read>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] + 130 | auto loaded = io.BinRead(is, component); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:262:35: required from here + 262 | reader.Read>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] + 130 | auto loaded = io.BinRead(is, component); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:265:41: required from here + 265 | reader.Read>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] + 130 | auto loaded = io.BinRead(is, component); + | ^~~~~~ +[ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -MF CMakeFiles/easel.dir/esl_gamma.c.o.d -o CMakeFiles/easel.dir/esl_gamma.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gamma.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 +[ 23%] Linking CXX static library libedlib.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake +/usr/bin/ar qc libgfa1.a CMakeFiles/gfa1.dir/gfa.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] + 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:14: note: did you mean to dereference the pointer? + 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] + 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:10: note: did you mean to dereference the pointer? + 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; + | ^ +[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -MF CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MemoryBuffer.cpp +/usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o +[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -MF CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d -o CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/NativeFormatting.cpp +[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Path.cpp +[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -MF CMakeFiles/llvm-support.dir/Process.cpp.o.d -o CMakeFiles/llvm-support.dir/Process.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp +/usr/bin/ranlib libgfa1.a +[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gencode.c +[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_getopts.c +/usr/bin/ranlib libedlib.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Program.cpp +[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c +[ 24%] Built target gfa1 +[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_histogram.c +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 25%] Built target edlib +make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence_tools.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hmm.c +[ 26%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp +[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o +cd 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CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp +[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hyperexp.c +[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SmallVector.cpp +[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_keyhash.c +[ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SourceMgr.cpp +[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mem.c +[ 27%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp +[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mixgev.c +[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -MF CMakeFiles/easel.dir/esl_mpi.c.o.d -o CMakeFiles/easel.dir/esl_mpi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mpi.c +[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringExtras.cpp +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here + 46 | void LoadImpl(BinIStream &str, Graph &graph) override { + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msa.c +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -MF CMakeFiles/easel.dir/esl_msacluster.c.o.d -o CMakeFiles/easel.dir/esl_msacluster.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msacluster.c +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -MF CMakeFiles/easel.dir/esl_msafile.c.o.d -o CMakeFiles/easel.dir/esl_msafile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringMap.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile2.c +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] + 94 | mi = ::mallinfo(); + | ~~~~~~~~~~^~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:35: +/usr/include/malloc.h:114:24: note: declared here + 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; + | ^~~~~~~~ +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -MF CMakeFiles/easel.dir/esl_msafile_a2m.c.o.d -o CMakeFiles/easel.dir/esl_msafile_a2m.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_a2m.c +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -MF CMakeFiles/llvm-support.dir/StringRef.cpp.o.d -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringRef.cpp +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -MF CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d -o CMakeFiles/llvm-support.dir/StringSaver.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringSaver.cpp +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ThreadLocal.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -MF CMakeFiles/easel.dir/esl_msafile_afa.c.o.d -o CMakeFiles/easel.dir/esl_msafile_afa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_afa.c +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -MF CMakeFiles/easel.dir/esl_msafile_clustal.c.o.d -o CMakeFiles/easel.dir/esl_msafile_clustal.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_clustal.c +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Threading.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -MF CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d -o CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/NativeFormatting.cpp -[ 37%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -2406,118 +2394,86 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Path.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 37%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp -[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Program.cpp -[ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Regex.cpp -[ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp -[ 38%] Linking C static library libeasel.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 -/usr/bin/ar qc libeasel.a CMakeFiles/easel.dir/easel.c.o CMakeFiles/easel.dir/esl_alphabet.c.o CMakeFiles/easel.dir/esl_avx.c.o CMakeFiles/easel.dir/esl_buffer.c.o CMakeFiles/easel.dir/esl_cluster.c.o CMakeFiles/easel.dir/esl_composition.c.o CMakeFiles/easel.dir/esl_dirichlet.c.o CMakeFiles/easel.dir/esl_distance.c.o CMakeFiles/easel.dir/esl_dmatrix.c.o CMakeFiles/easel.dir/esl_dsqdata.c.o CMakeFiles/easel.dir/esl_exponential.c.o CMakeFiles/easel.dir/esl_fileparser.c.o CMakeFiles/easel.dir/esl_gamma.c.o CMakeFiles/easel.dir/esl_gencode.c.o 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ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/TimeProfiler.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Twine.cpp +[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_phylip.c +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Unicode.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 38%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp -[ 38%] Built target easel -make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/CMakeFiles/hmmer.dir/DependInfo.cmake "--color=" -[ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SmallVector.cpp -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 39%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o -MF CMakeFiles/hmmer.dir/src/build.c.o.d -o CMakeFiles/hmmer.dir/src/build.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/build.c -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SourceMgr.cpp -[ 39%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o -MF CMakeFiles/hmmer.dir/src/cachedb.c.o.d -o CMakeFiles/hmmer.dir/src/cachedb.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/cachedb.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] - 94 | mi = ::mallinfo(); - | ~~~~~~~~~~^~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:35: -/usr/include/malloc.h:114:24: note: declared here - 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; - | ^~~~~~~~ -[ 39%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -MF CMakeFiles/hmmer.dir/src/emit.c.o.d -o CMakeFiles/hmmer.dir/src/emit.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/emit.c +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/WithColor.cpp +[ 33%] Linking CXX static library libformat.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake +[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -MF CMakeFiles/easel.dir/esl_msafile_psiblast.c.o.d -o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_psiblast.c +[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_selex.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 +/usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -MF CMakeFiles/easel.dir/esl_msafile_stockholm.c.o.d -o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_stockholm.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringExtras.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp:7: @@ -2525,142 +2481,166 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 40%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o -MF CMakeFiles/hmmer.dir/src/errors.c.o.d -o CMakeFiles/hmmer.dir/src/errors.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/errors.c -[ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringMap.cpp -[ 40%] Linking CXX static library libcoverage_model.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 -/usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -[ 40%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer 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/usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/YAMLTraits.cpp +[ 37%] Linking CXX static library libsequence.a +/usr/bin/ranlib libformat.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. 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CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o +/usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o +[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_os_ostream.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:97:9: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' + 97 | DeleteLink(w, e2); + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:109:33: required from here + 109 | helper.LinkEdges(e1, e2); + | ~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:102:14: warning: unused variable 'res' [-Wunused-variable] + 102 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); + | ^~~ +[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_normal.c +/usr/bin/ranlib libsequence.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 40%] Built target coverage_model +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 37%] Built target format +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +/usr/bin/ranlib libBamTools.a +[ 37%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o +[ 37%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration 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-isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_randomseq.c +[ 39%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regexec.c +[ 39%] Built target mimalloc-obj +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/genomic_info.cpp -[ 41%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_decoding.c -[ 41%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Threading.cpp -[ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/TimeProfiler.cpp -[ 43%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp -[ 43%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_recorder.c +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_rootfinder.c +[ 39%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regstrlcpy.c +[ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c +[ 40%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -MF CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d -o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp -[ 44%] Linking CXX static library libBamTools.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake -[ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Unicode.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && 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CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -[ 44%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_null2.c +[ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sq.c make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 44%] Built target BamTools +[ 40%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o +[ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio.c +[ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ascii.c +[ 40%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o +[ 41%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/temporary.cpp +[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/glob.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ncbi.c +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sse.c +[ 43%] Built target BamTools +[ 43%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && 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CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger_impl.cpp +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stack.c +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stats.c make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stopwatch.c +[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/kstring.c -[ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS 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Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_msv.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem 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-cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o -MF CMakeFiles/hmmer.dir/src/generic_optacc.c.o.d -o CMakeFiles/hmmer.dir/src/generic_optacc.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_optacc.c -[ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_os_ostream.cpp -[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o +[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -MF CMakeFiles/samtools.dir/bam_aux.c.o.d -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_aux.c -[ 46%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem 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CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_ostream.cpp -[ 46%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -MF CMakeFiles/hmmer.dir/src/generic_viterbi.c.o.d -o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_viterbi.c -[ 46%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -cd 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CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regcomp.c -[ 47%] Linking CXX static library libgraphio.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 -/usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o -[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE 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ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regerror.c -[ 48%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regexec.c -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 48%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -MF CMakeFiles/llvm-support.dir/regfree.c.o.d -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regfree.c -[ 48%] Built target graphio -[ 48%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp -[ 48%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regstrlcpy.c -[ 48%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -MF CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp -[ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_vtrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_vtrace.c -[ 48%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/glob.cpp -[ 50%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/temporary.cpp -[ 50%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp -[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o -MF CMakeFiles/hmmer.dir/src/h2_io.c.o.d -o CMakeFiles/hmmer.dir/src/h2_io.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/h2_io.c -[ 51%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -MF CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger_impl.cpp -[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o -MF CMakeFiles/hmmer.dir/src/heatmap.c.o.d -o CMakeFiles/hmmer.dir/src/heatmap.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/heatmap.c -[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -MF CMakeFiles/hmmer.dir/src/hmmlogo.c.o.d -o CMakeFiles/hmmer.dir/src/hmmlogo.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmlogo.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_threads.c +[ 44%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stretchexp.c +[ 44%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_tree.c +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c:23: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c: In function 'esl_scorematrix_Create': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.h:166:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 166 | if ( ((p) = malloc(size)) == NULL) { \ + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c:72:3: note: in expansion of macro 'ESL_ALLOC' + 72 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); + | ^~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.h:23: +/usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here + 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ + | ^~~~~~ +[ 44%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vectorops.c +[ 44%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -MF CMakeFiles/easel.dir/esl_vmx.c.o.d -o CMakeFiles/easel.dir/esl_vmx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vmx.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.c +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o +[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_workqueue.c +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -2673,36 +2653,23 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdwrkr.c -[ 52%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_wuss.c +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_import.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o -MF CMakeFiles/hmmer.dir/src/hmmdutils.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdutils.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdutils.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o -MF CMakeFiles/hmmer.dir/src/hmmer.c.o.d -o CMakeFiles/hmmer.dir/src/hmmer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmer.c -[ 53%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam.c.o -MF CMakeFiles/samtools.dir/sam.c.o.d -o CMakeFiles/samtools.dir/sam.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/sam.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -MF CMakeFiles/samtools.dir/bam_index.c.o.d -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -2721,10 +2688,8 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -MF CMakeFiles/hmmer.dir/src/logsum.c.o.d -o CMakeFiles/hmmer.dir/src/logsum.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/logsum.c -[ 53%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -MF CMakeFiles/samtools.dir/bam_index.c.o.d -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -MF CMakeFiles/samtools.dir/bam_pileup.c.o.d -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_pileup.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); @@ -2750,131 +2715,16 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o -MF CMakeFiles/hmmer.dir/src/modelconfig.c.o.d -o CMakeFiles/hmmer.dir/src/modelconfig.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/modelconfig.c -[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o -MF CMakeFiles/hmmer.dir/src/modelstats.c.o.d -o CMakeFiles/hmmer.dir/src/modelstats.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/modelstats.c -[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -MF CMakeFiles/hmmer.dir/src/mpisupport.c.o.d -o CMakeFiles/hmmer.dir/src/mpisupport.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/mpisupport.c -[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/seqmodel.c -[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -MF CMakeFiles/hmmer.dir/src/tracealign.c.o.d -o CMakeFiles/hmmer.dir/src/tracealign.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/tracealign.c -[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -MF CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o.d -o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_alidisplay.c -[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o -MF CMakeFiles/hmmer.dir/src/p7_bg.c.o.d -o CMakeFiles/hmmer.dir/src/p7_bg.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_bg.c -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o -MF CMakeFiles/hmmer.dir/src/p7_builder.c.o.d -o CMakeFiles/hmmer.dir/src/p7_builder.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_builder.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp:1: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 55%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -MF CMakeFiles/samtools.dir/bam_pileup.c.o.d -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_pileup.c -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -MF CMakeFiles/hmmer.dir/src/p7_domaindef.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_domaindef.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp:1: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/vector:63, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:12: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o -MF CMakeFiles/hmmer.dir/src/p7_gbands.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gbands.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gbands.c -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmx.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmx.c -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxb.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmxb.c -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmxchk.c -[ 56%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_lpileup.c -[ 58%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o +[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_md.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmm.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmm.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmm.c -[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmcache.c -[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmfile.c -[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmwindow.c -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o -MF CMakeFiles/hmmer.dir/src/p7_null3.c.o.d -o CMakeFiles/hmmer.dir/src/p7_null3.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_null3.c -[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -MF CMakeFiles/hmmer.dir/src/p7_pipeline.c.o.d -o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_pipeline.c -[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o -MF CMakeFiles/hmmer.dir/src/p7_prior.c.o.d -o CMakeFiles/hmmer.dir/src/p7_prior.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_prior.c -[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o -MF CMakeFiles/hmmer.dir/src/p7_profile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_profile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_profile.c -[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -cd 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -MF CMakeFiles/hmmer.dir/src/p7_spensemble.c.o.d -o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_spensemble.c -[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer 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-D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o -MF CMakeFiles/hmmer.dir/src/p7_tophits.c.o.d -o CMakeFiles/hmmer.dir/src/p7_tophits.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_tophits.c -[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o -MF CMakeFiles/hmmer.dir/src/p7_trace.c.o.d -o CMakeFiles/hmmer.dir/src/p7_trace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_trace.c -[ 60%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o +[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_lpileup.c +[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/razf.c.o -MF CMakeFiles/samtools.dir/razf.c.o.d -o CMakeFiles/samtools.dir/razf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c +[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/faidx.c +[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -MF CMakeFiles/samtools.dir/bedidx.c.o.d -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bedidx.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_flush': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); @@ -2916,72 +2766,122 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/faidx.c -[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include 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-o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmpgmd2msa.c -[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o -MF CMakeFiles/hmmer.dir/src/fm_general.c.o.d -o CMakeFiles/hmmer.dir/src/fm_general.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_general.c -[ 61%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_sse.c -[ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/fwdback.c -[ 61%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 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ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/mpi.c -[ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_reheader.c -[ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/kprobaln.c -[ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_cat.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +[ 50%] Linking CXX static library libgraphio.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 +/usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o 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[-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 50%] Built target graphio +/usr/bin/ranlib libcoverage_model.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 50%] Built target coverage_model +[ 50%] 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+cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem 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CMakeFiles/hmmer.dir/src/logsum.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/logsum.c +[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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/usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/seqmodel.c +[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -MF CMakeFiles/hmmer.dir/src/tracealign.c.o.d -o CMakeFiles/hmmer.dir/src/tracealign.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/tracealign.c +[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -MF CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o.d -o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_alidisplay.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -2989,7 +2889,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3002,72 +2901,200 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -MF CMakeFiles/hmmer.dir/src/p7_domaindef.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_domaindef.c +[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmwindow.c +[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o +[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o -MF CMakeFiles/hmmer.dir/src/p7_null3.c.o.d -o CMakeFiles/hmmer.dir/src/p7_null3.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_null3.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmfile.c +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -MF CMakeFiles/hmmer.dir/src/p7_pipeline.c.o.d -o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_pipeline.c +[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o -MF CMakeFiles/hmmer.dir/src/p7_prior.c.o.d -o CMakeFiles/hmmer.dir/src/p7_prior.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_prior.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -[ 65%] Linking CXX static library libsamtools.a +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o -MF CMakeFiles/hmmer.dir/src/p7_profile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_profile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_profile.c +[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include 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ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem 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Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/msvfilter.c +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/null2.c /usr/bin/ranlib libsamtools.a +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/optacc.c +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/vitfilter.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_omx.c make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 65%] Built target samtools -[ 65%] Linking CXX static library libllvm-support.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 -/usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" -/usr/bin/ranlib libllvm-support.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Built target llvm-support +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_oprofile.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/mpi.c +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/vector:63, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:12: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ [ 65%] Linking CXX static library libmapping_printer.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -P CMakeFiles/mapping_printer.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/mapping_printer.dir/link.txt --verbose=1 +/usr/bin/ar qc libmapping_printer.a CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o +/usr/bin/ranlib libmapping_printer.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 65%] Built target mapping_printer [ 65%] Linking CXX static library libutils.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake -/usr/bin/ar qc libmapping_printer.a CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" /usr/bin/ranlib libutils.a -/usr/bin/ranlib libmapping_printer.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 65%] Linking CXX static library libllvm-support.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake [ 65%] Built target utils +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 +/usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" +/usr/bin/ranlib libllvm-support.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 65%] Built target llvm-support make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Built target mapping_printer +[ 65%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o +[ 65%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o +[ 65%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o +[ 65%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o [ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection 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common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/id_distributor.cpp -[ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -[ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -[ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp -[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp -[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -MF CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d -o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp -[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3086,6 +3113,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:3, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: @@ -3094,99 +3130,54 @@ | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.hpp:7, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp:5: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.hpp:7, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 67%] Linking CXX static library ../../../lib/libgtest.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 -/usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" -/usr/bin/ranlib ../../../lib/libgtest.a -[ 67%] Linking CXX static library libConsensusCore.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 -[ 67%] Built target gtest -make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend -/usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build -[ 67%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated -O2 -MD -MT ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest_main.cc In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 67%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_gtest.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 67%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp -/usr/bin/ranlib libConsensusCore.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 67%] Built target ConsensusCore -make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp -[ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -[ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp -[ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp +[ 68%] Linking C static library libhmmer.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 +/usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o CMakeFiles/hmmer.dir/src/fm_general.c.o CMakeFiles/hmmer.dir/src/fm_sse.c.o CMakeFiles/hmmer.dir/src/fm_ssv.c.o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o +/usr/bin/ranlib libhmmer.a In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:9: @@ -3215,6 +3206,36 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:20:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' 20 | IdHolder edge_id_; | ^~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 68%] Built target hmmer +make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 68%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o +[ 68%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmfile.cpp +[ 68%] Linking CXX static library libpaired_info.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 +/usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o +/usr/bin/ranlib libpaired_info.a +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp:161:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 161 | pli->Z = pli->domZ = cfg.Z; + | ~~~~^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -3234,8 +3255,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, @@ -3249,8 +3268,10 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 580 | value_type tmp(std::forward(args)...); | ^~~ -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 68%] Built target paired_info +[ 68%] Linking CXX static library libhmmercpp.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -3258,6 +3279,8 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3270,6 +3293,8 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/usr/bin/ranlib libhmmercpp.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::RawPointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::RawPointT&}; T = omnigraph::de::RawPointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::RawPointT&; Args = {}; T = omnigraph::de::RawPointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, @@ -3283,47 +3308,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 8 into object 'tmp' of size 8 580 | value_type tmp(std::forward(args)...); | ^~~ -[ 68%] Linking CXX static library libteamcity_gtest.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 -[ 68%] Linking CXX static library ../../../lib/libgtest_main.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake -/usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 -/usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -/usr/bin/ranlib libteamcity_gtest.a -/usr/bin/ranlib ../../../lib/libgtest_main.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Built target teamcity_gtest -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp -[ 68%] Built target gtest_main -[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/extract_domains.cpp -[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp -[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(debruijn_graph::GraphPack&, const char*)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:27:9: warning: unused variable 'code' [-Wunused-variable] - 27 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); - | ^~~~ +[ 68%] Built target hmmercpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -3360,42 +3345,10 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 70%] Linking C static library libhmmer.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:10: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o CMakeFiles/hmmer.dir/src/fm_general.c.o CMakeFiles/hmmer.dir/src/fm_sse.c.o CMakeFiles/hmmer.dir/src/fm_ssv.c.o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -/usr/bin/ranlib libhmmer.a -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:14: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 70%] Built target hmmer -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 70%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmfile.cpp +[ 68%] Linking CXX static library libConsensusCore.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 +/usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -3418,11 +3371,204 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/usr/bin/ranlib libConsensusCore.a +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 68%] Linking CXX static library ../../../lib/libgtest.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 +[ 68%] Built target ConsensusCore +make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" +/usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o +[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp [ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/extract_domains.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp +[ 72%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp +/usr/bin/ranlib ../../../lib/libgtest.a +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 72%] Built target gtest +make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 72%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_gtest.cpp +[ 72%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp +[ 72%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated -O2 -MD -MT ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest_main.cc In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:10: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(debruijn_graph::GraphPack&, const char*)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:27:9: warning: unused variable 'code' [-Wunused-variable] + 27 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); + | ^~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 72%] Linking CXX static library ../../../lib/libgtest_main.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o +[ 72%] Linking CXX static library libteamcity_gtest.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 +/usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:12: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/usr/bin/ranlib libteamcity_gtest.a +/usr/bin/ranlib ../../../lib/libgtest_main.a +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ @@ -3437,48 +3583,49 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:8: +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 72%] Built target gtest_main +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 72%] Built target teamcity_gtest In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:9: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:61:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 61 | if (seqpos2.second - seqpos2.first < model_length / 10) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp: In function 'bool debruijn_graph::{anonymous}::CollectLibInformation(const debruijn_graph::GraphPack&, size_t&, size_t, size_t)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp:235:42: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 235 | if (data.median_insert_size < gp.k() + 2) + | ~~~~~~~^~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:17, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:10: @@ -3511,66 +3658,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:28:20: warning: unused parameter 'min_dist' [-Wunused-parameter] 28 | size_t min_dist, | ~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:12: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 70%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp -[ 70%] Linking CXX static library libpaired_info.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 -/usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp: In function 'bool debruijn_graph::{anonymous}::CollectLibInformation(const debruijn_graph::GraphPack&, size_t&, size_t, size_t)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp:235:42: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 235 | if (data.median_insert_size < gp.k() + 2) - | ~~~~~~~^~~ -[ 72%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp -/usr/bin/ranlib libpaired_info.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 72%] Built target paired_info -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp:161:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 161 | pli->Z = pli->domZ = cfg.Z; - | ~~~~^ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:457:14: warning: unused variable 'u1' [-Wunused-variable] @@ -3583,52 +3679,52 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:630:16: warning: unused variable 'cur_len' [-Wunused-variable] 630 | size_t cur_len = end_it - start_it; | ^~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:61:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 61 | if (seqpos2.second - seqpos2.first < model_length / 10) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 72%] Linking CXX static library libhmmercpp.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -/usr/bin/ranlib libhmmercpp.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 72%] Built target hmmercpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:216:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 216 | for (;index != res.first; ++index) { + | ~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:243:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 243 | if (coords.second + 5000 > path.Length()) { + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 72%] Linking CXX static library libbinary_io.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 +/usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' + 506 | queue_.pop(); + | ~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' + 251 | ++inner_it_; + | ^~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:362:64: required from here + 362 | for (auto edge = g_.SmartEdgeBegin(); !edge.IsEnd(); ++edge) { + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +/usr/bin/ranlib libbinary_io.a In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, @@ -3647,6 +3743,14 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 72%] Built target binary_io +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -3654,70 +3758,114 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o +[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o +[ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o +[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o +[ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/paired_readers.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/io_helper.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp +[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o +[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_converter.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/parser.cpp +[ 74%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o +[ 74%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/read.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -MF CMakeFiles/input.dir/sam/sam_reader.cpp.o.d -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/sam_reader.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:216:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 216 | for (;index != res.first; ++index) { - | ~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:243:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 243 | if (coords.second + 5000 > path.Length()) { - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 74%] Linking CXX static library libassembly_graph.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 +/usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o +/usr/bin/ranlib libassembly_graph.a In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' - 506 | queue_.pop(); - | ~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' - 251 | ++inner_it_; - | ^~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:362:64: required from here - 362 | for (auto edge = g_.SmartEdgeBegin(); !edge.IsEnd(); ++edge) { - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 74%] Built target assembly_graph +make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend +make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -MF CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d -o CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -MF CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d -o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -MF CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d -o CMakeFiles/path_extend.dir/overlap_remover.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); @@ -3737,53 +3885,12 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 72%] Linking CXX static library libbinary_io.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 -/usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o -/usr/bin/ranlib libbinary_io.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 72%] Built target binary_io -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.cpp -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/parser.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/paired_readers.cpp -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_converter.cpp -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/io_helper.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/read.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': @@ -3811,9 +3918,16 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 73%] Linking CXX static library libassembly_graph.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, @@ -3837,80 +3951,116 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -/usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -/usr/bin/ranlib libassembly_graph.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 73%] Built target assembly_graph -make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -MF CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d -o CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp -[ 75%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -MF CMakeFiles/input.dir/sam/sam_reader.cpp.o.d -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/sam_reader.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_set_params, std::allocator, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node, std::allocator, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/bits/alloc_traits.h:39, - from /usr/include/c++/14/ext/alloc_traits.h:34, - from /usr/include/c++/14/bits/hashtable_policy.h:39, - from /usr/include/c++/14/bits/hashtable.h:35, - from /usr/include/c++/14/bits/unordered_map.h:33, - from /usr/include/c++/14/unordered_map:41, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:7: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_set_params, std::allocator, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node, std::allocator, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_utils.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.hpp:14, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:13: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { @@ -3936,59 +4086,38 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/visualization/position_filler.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { @@ -4011,48 +4140,46 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -MF CMakeFiles/modules.dir/chromosome_remover.cpp.o.d -o CMakeFiles/modules.dir/chromosome_remover.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp:9: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:277:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 277 | if (bad_mapping_pos == -1) + | ~~~~~~~~~~~~~~~~^~~~~ +[ 81%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ @@ -4066,111 +4193,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -MF CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d -o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', - inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, - inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, - inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, - inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, - inlined from 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_filters.hpp:257:32: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 - 580 | value_type tmp(std::forward(args)...); - | ^~~ -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:10: -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/streambuf:43, - from /usr/include/c++/14/bits/streambuf_iterator.h:35, - from /usr/include/c++/14/iterator:66, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/iterator.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/iterator/iterator_facade.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/chained_iterator.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:8: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -4178,20 +4209,18 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_utils.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:29:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] + 29 | if (sum < absolute_weight_threshold_) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': @@ -4201,80 +4230,24 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -MF CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d -o CMakeFiles/path_extend.dir/overlap_remover.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:3, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:3, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ @@ -4282,9 +4255,9 @@ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_set_params, std::allocator, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node, std::allocator, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, @@ -4298,23 +4271,23 @@ from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:7: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_set_params, std::allocator, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node, std::allocator, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, @@ -4326,79 +4299,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/visualization/position_filler.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -MF CMakeFiles/modules.dir/alignment/gap_info.cpp.o.d -o CMakeFiles/modules.dir/alignment/gap_info.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -MF CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d -o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' - 506 | queue_.pop(); - | ~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' - 251 | ++inner_it_; - | ^~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:34:58: required from here - 34 | for (auto it = g.SmartVertexBegin(); ! it.IsEnd(); ++it) { - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' - 506 | queue_.pop(); - | ~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' - 251 | ++inner_it_; - | ^~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:131:64: required from here - 131 | for (auto iter = graph.SmartEdgeBegin(); ! iter.IsEnd(); ++iter) { - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4417,53 +4317,29 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp -[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp -[ 76%] Linking CXX static library libinput.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 -/usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o -/usr/bin/ranlib libinput.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 76%] Built target input -[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here - 597 | virtual void HandleMerge(const std::vector &old_edges, EdgeId new_edge) override { - | ^~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] - 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4476,75 +4352,30 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = nrps::DomainGraphDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = nrps::DomainGraphDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = nrps::DomainGraphDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', - inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, - inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, - inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, - inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, - inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, - inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, - inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, - inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, - inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:168:43: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 - 580 | value_type tmp(std::forward(args)...); - | ^~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', - inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, - inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, - inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, - inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, - inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, - inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, - inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, - inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, - inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:170:43: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 - 580 | value_type tmp(std::forward(args)...); - | ^~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4557,6 +4388,13 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:111:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] + 111 | if (iter->second < min_read_count_) { + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4565,54 +4403,31 @@ | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -4620,24 +4435,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 79%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp -[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:277:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 277 | if (bad_mapping_pos == -1) - | ~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': @@ -4647,8 +4444,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4667,75 +4462,24 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:29:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] - 29 | if (sum < absolute_weight_threshold_) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp -[ 79%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp: In static member function 'static int path_extend::ExtenderTriplet::GetPriority(io::LibraryType)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority @@ -4881,12 +4625,62 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:46:13: note: in expansion of macro 'SET_PRIORITY' 46 | SET_PRIORITY(LibraryType::AssemblyGraph); | ^~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' + 506 | queue_.pop(); + | ~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' + 251 | ++inner_it_; + | ^~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:34:58: required from here + 34 | for (auto it = g.SmartVertexBegin(); ! it.IsEnd(); ++it) { + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' + 506 | queue_.pop(); + | ~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' + 251 | ++inner_it_; + | ^~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:131:64: required from here + 131 | for (auto iter = graph.SmartEdgeBegin(); ! iter.IsEnd(); ++iter) { + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', + inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, + inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, + inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, + inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, + inlined from 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_filters.hpp:257:32: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 + 580 | value_type tmp(std::forward(args)...); + | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4899,29 +4693,137 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp -[ 80%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:10: +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/streambuf:43, + from /usr/include/c++/14/bits/streambuf_iterator.h:35, + from /usr/include/c++/14/iterator:66, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/iterator.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/iterator/iterator_facade.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/chained_iterator.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:8: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here + 597 | virtual void HandleMerge(const std::vector &old_edges, EdgeId new_edge) override { + | ^~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] + 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/bits/alloc_traits.h:39, + from /usr/include/c++/14/ext/alloc_traits.h:34, + from /usr/include/c++/14/bits/hashtable_policy.h:39, + from /usr/include/c++/14/bits/hashtable.h:35, + from /usr/include/c++/14/bits/unordered_map.h:33, + from /usr/include/c++/14/unordered_map:41, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4940,82 +4842,45 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:3, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:3, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 81%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.hpp:14, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:111:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] - 111 | if (iter->second < min_read_count_) { - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 81%] Linking CXX static library libinput.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 +/usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = nrps::DomainGraphDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = nrps::DomainGraphDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = nrps::DomainGraphDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -5028,19 +4893,51 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -5076,6 +4973,160 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +/usr/bin/ranlib libinput.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 81%] Built target input +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', + inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, + inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, + inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, + inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, + inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, + inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, + inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, + inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, + inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:168:43: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 + 580 | value_type tmp(std::forward(args)...); + | ^~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', + inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, + inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, + inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, + inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, + inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, + inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, + inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, + inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, + inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:170:43: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 + 580 | value_type tmp(std::forward(args)...); + | ^~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -5104,17 +5155,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -5133,6 +5174,82 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -5171,10 +5288,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -5182,14 +5295,12 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -5218,6 +5329,25 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -5240,44 +5370,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -5310,7 +5402,7 @@ from /usr/include/c++/14/string:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: @@ -5328,93 +5420,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -5428,7 +5433,7 @@ from /usr/include/c++/14/string:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:8: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: @@ -5468,12 +5473,29 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 81%] Linking CXX static library libmodules.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 -/usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/alignment/gap_info.cpp.o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -/usr/bin/ranlib libmodules.a -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -5492,6 +5514,24 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +[ 81%] Linking CXX static library libmodules.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 +/usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/alignment/gap_info.cpp.o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o +/usr/bin/ranlib libmodules.a +[ 81%] Linking CXX static library libpath_extend.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 +/usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/pe_config_struct.cpp.o CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target modules /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': @@ -5573,15 +5613,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 81%] Linking CXX static library libspades-stages.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 -/usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" -[ 81%] Linking CXX static library libpath_extend.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 -/usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/pe_config_struct.cpp.o CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -/usr/bin/ranlib libspades-stages.a /usr/bin/ranlib libpath_extend.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target path_extend @@ -5592,17 +5623,15 @@ make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o +[ 81%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o +[ 81%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -MF CMakeFiles/pipeline.dir/config_struct.cpp.o.d -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/config_struct.cpp -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -MF CMakeFiles/pipeline.dir/library.cpp.o.d -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -MF CMakeFiles/pipeline.dir/library_data.cpp.o.d -o CMakeFiles/pipeline.dir/library_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library_data.cpp [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o +[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -MF CMakeFiles/pipeline.dir/stage.cpp.o.d -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -MF CMakeFiles/pipeline.dir/library.cpp.o.d -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.cpp -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 82%] Built target spades-stages In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:8: @@ -5662,6 +5691,10 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ +[ 82%] Linking CXX static library libspades-stages.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 +/usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': @@ -5719,6 +5752,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ +/usr/bin/ranlib libspades-stages.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 82%] Built target spades-stages /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -5829,49 +5865,49 @@ make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/construction.cpp.o -MF CMakeFiles/stages.dir/construction.cpp.o.d -o CMakeFiles/stages.dir/construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp +[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o [ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o +[ 83%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o +[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -MF CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/subcluster.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -MF CMakeFiles/stages.dir/read_conversion.cpp.o.d -o CMakeFiles/stages.dir/read_conversion.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/read_conversion.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/construction.cpp.o -MF CMakeFiles/stages.dir/construction.cpp.o.d -o CMakeFiles/stages.dir/construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp +[ 84%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -MF CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/subcluster.cpp -[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -[ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/err_helper_table.cpp -[ 83%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -MF CMakeFiles/stages.dir/ss_edge_split.cpp.o.d -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common 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CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d -o CMakeFiles/stages.dir/genomic_info_filler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/genomic_info_filler.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/err_helper_table.cpp +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG 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projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_helpers.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -MF CMakeFiles/stages.dir/ss_edge_split.cpp.o.d -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -MF CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/config_struct.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o -MF CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d -o CMakeFiles/stages.dir/genomic_info_filler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/genomic_info_filler.cpp +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer 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projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -MF CMakeFiles/spades-ionhammer.dir/reference.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/reference.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o -MF CMakeFiles/spades-ionhammer.dir/main.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -MF CMakeFiles/spades-ionhammer.dir/reference.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/reference.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp -[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/quality_thresholds_estimator.cpp -[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -MF CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/hamcluster_1.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:85:76: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 85 | transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate); @@ -5921,16 +5957,16 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:11: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ @@ -5995,34 +6031,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:11: @@ -6101,6 +6109,24 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:17, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:17: @@ -6213,6 +6239,16 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] 53 | size_t cnt = border_.erase(v); | ^~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': @@ -6501,133 +6537,206 @@ make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake "--color=" +make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake "--color=" -make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake "--color=" +make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" -make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/depend -make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/depend make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend +make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" +make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake "--color=" -make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/depend -make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/depend make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/depend -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' 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directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake "--color=" +make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/form_truealignments.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis/CMakeFiles/mag-improve.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build +make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build +make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build +make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make 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'/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 86%] Building CXX object projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -[ 86%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -MF CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o.d -o CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter/convert_bin_to_fasta.cpp +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build +make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/build +make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build +make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build +make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build -[ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -MF CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o.d -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -MF CMakeFiles/spades-hammer.dir/main.cpp.o.d -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/main.cpp make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/build -[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o +[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o +[ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o +[ 88%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o +[ 88%] Building CXX object projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o +[ 88%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o +[ 88%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o +[ 89%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o +[ 89%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o +[ 89%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o +[ 89%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o +[ 90%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o +[ 90%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o +[ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/interesting_pos_processor.cpp +[ 91%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -MF CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o.d -o CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/kmer_estimating.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp +[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -MF CMakeFiles/spades-gbuilder.dir/main.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o.d -o CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter/convert_bin_to_fasta.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -MF CMakeFiles/unitig-coverage.dir/main.cpp.o.d -o CMakeFiles/unitig-coverage.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/dataset_processor.cpp +[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -MF CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/positional_read.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -MF CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o.d -o CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp +[ 91%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/config_struct.cpp cd 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-ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -MF CMakeFiles/spades-core.dir/main.cpp.o.d -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/main.cpp -[ 86%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -[ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -[ 87%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/main.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp +[ 93%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o +[ 93%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o +[ 93%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -MF CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o.d -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp +[ 94%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o +[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem 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CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/mts/contig_abundance.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -MF CMakeFiles/spades-kmercount.dir/main.cpp.o.d -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp -[ 86%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_data.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/main.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp +[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o +[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/config_struct_hammer.cpp +[ 93%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o +[ 94%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp -[ 88%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/mts/contig_abundance.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/interesting_pos_processor.cpp -[ 89%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -[ 89%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -[ 89%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp -[ 90%] Building CXX object projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 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CMakeFiles/spaligner.dir/align_longreads.cpp.o.d -o CMakeFiles/spaligner.dir/align_longreads.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp +[ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o +[ 96%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o -MF CMakeFiles/mag-improve.dir/main.cpp.o.d -o CMakeFiles/mag-improve.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -MF CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -MF CMakeFiles/spades-read-filter.dir/read_filter.cpp.o.d -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/read_filter.cpp -[ 91%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -[ 93%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -MF CMakeFiles/spades-gbuilder.dir/main.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp -[ 93%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -MF CMakeFiles/unitig-coverage.dir/main.cpp.o.d -o CMakeFiles/unitig-coverage.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp -[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/dataset_processor.cpp +[ 96%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -MF CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -MF CMakeFiles/cds-subgraphs.dir/main.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp +[ 96%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -MF CMakeFiles/cds-mapping-stats.dir/stats.cpp.o.d -o CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -MF CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o.d -o CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/expander.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp:72:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] + 72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; + | ~~~~~~~~~~^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp: In instantiation of 'void parallel_radix_sort::value_manager::PairValueManager::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:543:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' @@ -6672,19 +6781,32 @@ 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 357 | for (uint32_t j=0; j::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: @@ -6693,16 +6815,24 @@ | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp:11: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:21, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ @@ -6711,6 +6841,35 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp:135:19: warning: unused variable 'mode' [-Wunused-variable] 135 | pipeline_type mode = cfg::get().mode; | ^~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:21, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 357 | for (uint32_t j=0; j::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp: In member function 'bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map&) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:65: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { @@ -6718,16 +6877,26 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here - 197 | debruijn_graph::FastGraphFromSequencesConstructor(k, ext_index).ConstructGraph(g, edge_sequences); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 488 | graph.ereserve(size_t(2.01*sequences.size())); - | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 504 | graph.vreserve(size_t(2.01*size)); - | ^~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In member function 'bin_refinement::EdgeSet bin_refinement::BoundedRegionsExpander::ProcessComponent(const bin_refinement::VertexSet&, const bin_refinement::EdgeSet&, const bin_refinement::EdgeSet&) const': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:248:47: warning: unused parameter 'reached' [-Wunused-parameter] + 248 | EdgeSet ProcessComponent(const VertexSet &reached, + | ~~~~~~~~~~~~~~~~~^~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::BoundedRegionsExpander::BoundedRegionsExpander(const debruijn_graph::Graph&, const std::set, std::allocator >&, size_t)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:275:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] + 275 | for (EdgeId e : annotated) { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::OnlyAnnotatedReachableExpander::OnlyAnnotatedReachableExpander(const debruijn_graph::Graph&, const bin_refinement::EdgeSet&, size_t, double, double, const std::string&)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:465:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] + 465 | for (EdgeId e : annotated) { + | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:29: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:457:14: warning: unused variable 'u1' [-Wunused-variable] @@ -6740,11 +6909,23 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:630:16: warning: unused variable 'cur_len' [-Wunused-variable] 630 | size_t cur_len = end_it - start_it; | ^~~~~~~ -[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/config_struct.cpp -[ 94%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -MF CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o.d -o CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here + 197 | debruijn_graph::FastGraphFromSequencesConstructor(k, ext_index).ConstructGraph(g, edge_sequences); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 488 | graph.ereserve(size_t(2.01*sequences.size())); + | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 504 | graph.vreserve(size_t(2.01*size)); + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp: In function 'void debruijn::simplification::Simplify(debruijn_graph::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] + 103 | const bool using_edge_qual = edge_qual.IsAttached(); + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { @@ -6798,8 +6979,23 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/main.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here + 29 | bool Load(const std::string &basename, Graph &graph) override { + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here + 42 | bool BinRead(std::istream &is, Graph &graph) override { + | ^~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { @@ -6810,15 +7006,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_data.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': @@ -6840,25 +7036,22 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here + 29 | bool Load(const std::string &basename, Graph &graph) override { + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here + 42 | bool BinRead(std::istream &is, Graph &graph) override { + | ^~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { @@ -6869,8 +7062,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/config_struct_hammer.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': @@ -6880,256 +7071,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:548, - from /usr/include/c++/14/cstring:43, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/mpmc_bounded.hpp:44, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/read_processor.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:12: -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, - inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, - inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2873:46, - inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2895:39, - inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, - inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, - inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, - inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, - inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, - inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, - inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, - inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 6 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 48 into object 'kmer' of size 40 - 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; - | ^~~~ -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, - inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, - inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2874:46, - inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2895:39, - inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, - inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, - inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, - inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, - inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, - inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, - inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, - inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 7 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 56 into object 'kmer' of size 40 - 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; - | ^~~~ -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, - inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, - inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2873:46, - inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2896:39, - inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, - inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, - inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, - inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, - inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, - inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, - inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, - inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 'long unsigned int[4]' is partly outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset [33, 40] into object 'kmer' of size 40 - 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; - | ^~~~ -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, - inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, - inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2874:46, - inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2896:39, - inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, - inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, - inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, - inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, - inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, - inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, - inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, - inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript [5, 6] is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset [41, 48] into object 'kmer' of size 40 - 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; - | ^~~~ -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, - inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, - inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2874:46, - inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2898:35, - inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, - inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, - inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, - inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, - inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, - inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, - inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, - inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 5 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 40 into object 'kmer' of size 40 - 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; - | ^~~~ -[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/expander.cpp -make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/form_truealignments.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 94%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -MF CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o.d -o CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp -make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 94%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 94%] Linking CXX executable ../../bin/spades-core -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm -[ 95%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/main.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp -make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -MF CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp -[ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -MF CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp -[ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -MF CMakeFiles/cds-subgraphs.dir/main.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp:72:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] - 72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; - | ~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 95%] Linking CXX executable ../../bin/spades-truseq-scfcorrection -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 96%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -MF CMakeFiles/cds-mapping-stats.dir/stats.cpp.o.d -o CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 96%] Linking CXX executable ../../bin/spades-corrector-core -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target spades-truseq-scfcorrection -make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis/CMakeFiles/mag-improve.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 96%] Building CXX object projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o -MF CMakeFiles/mag-improve.dir/main.cpp.o.d -o CMakeFiles/mag-improve.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp: In function 'void debruijn::simplification::Simplify(debruijn_graph::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] - 103 | const bool using_edge_qual = edge_qual.IsAttached(); - | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target spades-corrector-core -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { @@ -7144,7 +7088,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ -[ 96%] Linking CXX executable ../../bin/spades-kmer-estimating In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here @@ -7156,20 +7099,17 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target spades-kmer-estimating -[ 96%] Built target spades-core -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here + 46 | void LoadImpl(BinIStream &str, Graph &graph) override { + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': @@ -7179,44 +7119,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In member function 'bin_refinement::EdgeSet bin_refinement::BoundedRegionsExpander::ProcessComponent(const bin_refinement::VertexSet&, const bin_refinement::EdgeSet&, const bin_refinement::EdgeSet&) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:248:47: warning: unused parameter 'reached' [-Wunused-parameter] - 248 | EdgeSet ProcessComponent(const VertexSet &reached, - | ~~~~~~~~~~~~~~~~~^~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::BoundedRegionsExpander::BoundedRegionsExpander(const debruijn_graph::Graph&, const std::set, std::allocator >&, size_t)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:275:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] - 275 | for (EdgeId e : annotated) { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::OnlyAnnotatedReachableExpander::OnlyAnnotatedReachableExpander(const debruijn_graph::Graph&, const bin_refinement::EdgeSet&, size_t, double, double, const std::string&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:465:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] - 465 | for (EdgeId e : annotated) { - | ^ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:20: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here - 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] - 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { - | ~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:21: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here - 29 | bool Load(const std::string &basename, Graph &graph) override { - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here - 42 | bool BinRead(std::istream &is, Graph &graph) override { - | ^~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { @@ -7227,6 +7129,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': @@ -7293,9 +7204,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] 53 | size_t cnt = border_.erase(v); | ^~~ -[ 96%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:12: @@ -7335,6 +7252,42 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:20: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here + 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] + 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { + | ~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:21: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here + 29 | bool Load(const std::string &basename, Graph &graph) override { + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here + 42 | bool BinRead(std::istream &is, Graph &graph) override { + | ^~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here + 46 | void LoadImpl(BinIStream &str, Graph &graph) override { + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': @@ -7385,35 +7338,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here - 29 | bool Load(const std::string &basename, Graph &graph) override { - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here - 42 | bool BinRead(std::istream &is, Graph &graph) override { - | ^~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here - 46 | void LoadImpl(BinIStream &str, Graph &graph) override { - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target spades-convert-bin-to-fasta In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': @@ -7423,93 +7347,205 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/string.h:548, + from /usr/include/c++/14/cstring:43, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/mpmc_bounded.hpp:44, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/read_processor.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:12: +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, + inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, + inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2873:46, + inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2895:39, + inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, + inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, + inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, + inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, + inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, + inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, + inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, + inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 6 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 48 into object 'kmer' of size 40 + 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; + | ^~~~ +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, + inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, + inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2874:46, + inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2895:39, + inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, + inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, + inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, + inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, + inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, + inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, + inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, + inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 7 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 56 into object 'kmer' of size 40 + 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; + | ^~~~ +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, + inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, + inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2873:46, + inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2896:39, + inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, + inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, + inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, + inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, + inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, + inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, + inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, + inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 'long unsigned int[4]' is partly outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset [33, 40] into object 'kmer' of size 40 + 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; + | ^~~~ +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, + inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, + inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2874:46, + inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2896:39, + inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, + inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, + inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, + inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, + inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, + inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, + inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, + inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript [5, 6] is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset [41, 48] into object 'kmer' of size 40 + 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; + | ^~~~ +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, + inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, + inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2874:46, + inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2898:35, + inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, + inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, + inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, + inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, + inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, + inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, + inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, + inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 5 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 40 into object 'kmer' of size 40 + 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; + | ^~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +[ 96%] Linking CXX executable ../../bin/spades-core +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm +[ 96%] Linking CXX executable ../../bin/spades-truseq-scfcorrection +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +[ 96%] Linking CXX executable ../../bin/spades-corrector-core +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target spades-corrector-core +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target spades-truseq-scfcorrection +[ 96%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target spades-core +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target spades-convert-bin-to-fasta +[ 97%] Linking CXX executable ../../bin/spades-hammer +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target spades-hammer +[ 97%] Linking CXX executable ../../bin/spades-kmer-estimating +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target spades-kmer-estimating /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here - 29 | bool Load(const std::string &basename, Graph &graph) override { - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here - 42 | bool BinRead(std::istream &is, Graph &graph) override { - | ^~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here - 46 | void LoadImpl(BinIStream &str, Graph &graph) override { - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 96%] Linking CXX executable ../../bin/spades-kmercount -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target spades-kmercount +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7555,9 +7591,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -[ 97%] Linking CXX executable ../../bin/spades-hammer -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] @@ -7567,13 +7600,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target spades-hammer -[ 98%] Linking CXX executable ../../bin/spades-read-filter -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spades-read-filter /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7601,21 +7627,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -[ 98%] Linking CXX executable ../../bin/unitig-coverage +[ 97%] Linking CXX executable ../../bin/unitig-coverage cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitig-coverage.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/unitig-coverage.dir/main.cpp.o" "CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/unitig-coverage ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -[ 98%] Linking CXX executable ../../bin/spaligner -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/spaligner.dir/align_longreads.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spaligner libmapping_printer.a ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target unitig-coverage -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spaligner -[ 98%] Linking CXX executable ../../bin/spades-gmapper -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gmapper.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/easel/libeasel.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spades-gmapper /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7634,6 +7648,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 98%] Linking CXX executable ../../bin/spades-read-filter +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] @@ -7643,6 +7660,13 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target unitig-coverage +[ 98%] Linking CXX executable ../../bin/spades-kmercount +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target spades-read-filter /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7670,6 +7694,28 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target spades-kmercount +[ 98%] Linking CXX executable ../../bin/spades-gmapper +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gmapper.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/easel/libeasel.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +[100%] Linking CXX executable ../../bin/cds-subgraphs +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o" "CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o" "CMakeFiles/cds-subgraphs.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-subgraphs ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +[100%] Linking CXX executable ../../bin/form_truealignments +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/form_truealignments.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/form_truealignments ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[100%] Built target spades-gmapper +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[100%] Built target form_truealignments +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[100%] Linking CXX executable ../../bin/spaligner +[100%] Built target cds-subgraphs +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/spaligner.dir/align_longreads.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spaligner libmapping_printer.a ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[100%] Built target spaligner /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7688,25 +7734,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable ../../bin/form_truealignments -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/form_truealignments.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/form_truealignments ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target form_truealignments -[100%] Linking CXX executable ../../bin/cds-subgraphs -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o" "CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o" "CMakeFiles/cds-subgraphs.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-subgraphs ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[100%] Built target cds-subgraphs /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7734,16 +7761,20 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ [100%] Linking CXX executable ../../bin/cds-mapping-stats cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-mapping-stats.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-mapping-stats.dir/stats.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-mapping-stats ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target cds-mapping-stats -[100%] Linking CXX executable ../../bin/spades-gbuilder -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gbuilder.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[100%] Built target spades-gbuilder /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7771,6 +7802,11 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ +[100%] Linking CXX executable ../../bin/spades-gbuilder +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gbuilder.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[100%] Built target spades-gbuilder [100%] Linking CXX executable ../../bin/mag-improve cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/cmake -E cmake_link_script CMakeFiles/mag-improve.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/mag-improve.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/mag-improve ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so @@ -7790,249 +7826,236 @@ make -f CMakeFiles/Makefile2 test/debruijn/CMakeFiles/debruijn_test.dir/all make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" -Dependencies file "common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". -Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/compiler_depend.internal". -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" -Consolidate compiler generated dependencies of target mimalloc-obj +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" +Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/compiler_depend.internal". +Dependencies file "common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". +Dependencies file "ext/cppformat/CMakeFiles/format.dir/format.cc.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". +Dependencies file "ext/cppformat/CMakeFiles/format.dir/posix.cc.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". +Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/cppformat/CMakeFiles/format.dir/format.cc.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". -make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" -Dependencies file "ext/cppformat/CMakeFiles/format.dir/posix.cc.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target coverage_model +Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". +Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". +Dependencies file "common/utils/CMakeFiles/version.dir/version.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target format -Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target gqf Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build -Consolidate compiler generated dependencies of target edlib +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target gtest Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". -Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". -Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". -Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "common/utils/CMakeFiles/version.dir/version.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target version -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target binary_io Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target paired_info -[ 2%] Built target mimalloc-obj -[ 4%] Built target format Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 7%] Built target edlib Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 9%] Built target gqf Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 9%] Built target coverage_model -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target gqf +Consolidate compiler generated dependencies of target mimalloc-obj +Consolidate compiler generated dependencies of target gtest +Consolidate compiler generated dependencies of target paired_info +Consolidate compiler generated dependencies of target format +Consolidate compiler generated dependencies of target binary_io +Consolidate compiler generated dependencies of target coverage_model +Consolidate compiler generated dependencies of target edlib +Consolidate compiler generated dependencies of target BamTools +Consolidate compiler generated dependencies of target version +Consolidate compiler generated dependencies of target llvm-support +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build +make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build +make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. +make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 9%] Built target gtest make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. +make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" -[ 11%] Built target version -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend -Consolidate compiler generated dependencies of target BamTools +make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 11%] Built target binary_io -make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" -Dependencies file "common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/compiler_depend.internal". -[ 11%] Built target paired_info -Consolidate compiler generated dependencies of target sequence +make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. +make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 4%] Built target gqf +[ 7%] Built target mimalloc-obj +[ 7%] Built target edlib +[ 9%] Built target version +[ 9%] Built target gtest +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend +[ 11%] Built target format +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +[ 11%] Built target paired_info +[ 11%] Built target coverage_model +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +[ 11%] Built target binary_io +[ 30%] Built target BamTools +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" +[ 52%] Built target llvm-support Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". +Dependencies file "common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target teamcity_gtest Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 30%] Built target BamTools -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" -[ 33%] Built target sequence -Consolidate compiler generated dependencies of target llvm-support -Consolidate compiler generated dependencies of target utils -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 33%] Built target teamcity_gtest -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". @@ -8049,104 +8072,117 @@ Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kstring.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/razf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target teamcity_gtest +Consolidate compiler generated dependencies of target utils +Consolidate compiler generated dependencies of target sequence Consolidate compiler generated dependencies of target samtools make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build -[ 57%] Built target llvm-support -[ 35%] Built target utils +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd 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Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target modules +Consolidate compiler generated dependencies of target path_extend make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 78%] Built target modules -Consolidate compiler generated dependencies of target path_extend -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 78%] Built target modules [ 88%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -8195,41 +8231,40 @@ make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -MF CMakeFiles/debruijn_test.dir/histogram_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/histogram_test.cpp [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -MF CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_analysis_test.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -MF CMakeFiles/debruijn_test.dir/simplification_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_analysis_test.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -MF CMakeFiles/debruijn_test.dir/histogram_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/histogram_test.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o +[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o +[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem 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test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -MF CMakeFiles/debruijn_test.dir/graphio.cpp.o.d -o CMakeFiles/debruijn_test.dir/graphio.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem 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-Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -MF CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -MF CMakeFiles/debruijn_test.dir/test.cpp.o.d -o CMakeFiles/debruijn_test.dir/test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ @@ -8242,41 +8277,35 @@ | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:7: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:9: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ @@ -8296,6 +8325,13 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:128:24: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 128 | EdgeId new_id = graph.AddEdge(start_id, fin_id, Graph::EdgeData(tmp), eid, conj_eid); | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadPositions(const std::string&, omnigraph::EdgesPositionHandler&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:193:13: warning: variable 'read_count' set but not used [-Wunused-but-set-variable] 193 | int read_count = fscanf(file, "%zu\n", &pos_count); @@ -8315,6 +8351,22 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 415 | ObservableGraph::~ObservableGraph() { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': @@ -8339,15 +8391,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); @@ -8364,13 +8407,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 415 | ObservableGraph::~ObservableGraph() { - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:104:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 104 | gap_cfg.penalty_ratio = 0.1; @@ -8389,6 +8434,25 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:191:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 191 | gap_cfg.penalty_ratio = 0.1; | ^~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:10: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here + 46 | void LoadImpl(BinIStream &str, Graph &graph) override { + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here + 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] + 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { + | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': @@ -8435,50 +8499,32 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:14: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' + 547 | FastGraphFromSequencesConstructor(kmer_size_, origin_).ConstructGraph(graph_, edge_sequences); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' + 59 | g_c.ConstructGraph(params.keep_perfect_loops); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' + 68 | return ConstructGraphUsingExtensionIndex(params, workdir, streams, g); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:77:37: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphWithIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&, EdgeIndex&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' + 77 | KMerFiles kmers = ConstructGraph(params, workdir, streams, g); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:75:28: required from here + 75 | ConstructGraphWithIndex(config::debruijn_config::construction(), workdir, streams, graph, index); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 488 | graph.ereserve(size_t(2.01*sequences.size())); + | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 504 | graph.vreserve(size_t(2.01*size)); + | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:10: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here - 46 | void LoadImpl(BinIStream &str, Graph &graph) override { - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here - 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] - 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { - | ~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -8486,13 +8532,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -8517,13 +8556,6 @@ | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -8551,48 +8583,36 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:14: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' - 547 | FastGraphFromSequencesConstructor(kmer_size_, origin_).ConstructGraph(graph_, edge_sequences); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' - 59 | g_c.ConstructGraph(params.keep_perfect_loops); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' - 68 | return ConstructGraphUsingExtensionIndex(params, workdir, streams, g); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:77:37: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphWithIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&, EdgeIndex&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' - 77 | KMerFiles kmers = ConstructGraph(params, workdir, streams, g); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:75:28: required from here - 75 | ConstructGraphWithIndex(config::debruijn_config::construction(), workdir, streams, graph, index); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 488 | graph.ereserve(size_t(2.01*sequences.size())); - | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 504 | graph.vreserve(size_t(2.01*size)); - | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -8609,6 +8629,13 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': @@ -8627,18 +8654,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -8696,6 +8714,33 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12: @@ -8724,31 +8769,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': @@ -8815,22 +8835,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] 53 | size_t cnt = border_.erase(v); | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:720:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' @@ -8876,24 +8880,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:43:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 43 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:813:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' @@ -8914,6 +8900,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:777:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 777 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'omnigraph::complex_br::ComponentProjector::EdgeId omnigraph::complex_br::ComponentProjector::CorrespondingTreeEdge(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:824:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 824 | EdgeId target = CorrespondingTreeEdge(*it); @@ -8933,6 +8928,29 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:793:16: warning: unused variable 'end_height' [-Wunused-variable] 793 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); @@ -9004,6 +9022,8 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:244:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 244 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -9023,6 +9043,19 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -9042,6 +9075,18 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -9070,9 +9115,18 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -9111,6 +9165,25 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -9133,25 +9206,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -9171,7 +9225,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -9190,6 +9244,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -9227,26 +9282,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -9265,6 +9300,16 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -9292,15 +9337,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -9449,6 +9485,25 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -9471,6 +9526,15 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -9493,34 +9557,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -9587,166 +9623,166 @@ make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info 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'/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd 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ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. +make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. +make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build -make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build +make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build -[ 19%] Built target BamTools make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. +make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. +make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 21%] Built target edlib -[ 21%] Built target coverage_model -[ 24%] Built target format -[ 26%] Built target gqf -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend -[ 29%] Built target mimalloc-obj -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 31%] Built target BamTools make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend -[ 51%] Built target binary_io -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +[ 53%] Built target llvm-support make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build +make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 53%] Built target sequence +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build +[ 56%] Built target sequence +[ 56%] Built target teamcity_gtest make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. +make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 56%] Built target version -[ 63%] Built target samtools -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +[ 58%] Built target utils +make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend +[ 65%] Built target samtools make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -[ 63%] Built target paired_info -[ 63%] Built target teamcity_gtest make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. +make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Built target utils -make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend -[ 70%] Built target input -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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assembly_graph make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -9789,18 +9825,18 @@ make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o +[ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/sequence_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/sequence_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/quality_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -MF CMakeFiles/include_test.dir/nucl_test.cpp.o.d -o CMakeFiles/include_test.dir/nucl_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/nucl_test.cpp -[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -MF CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o.d -o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/cyclic_hash_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/binary_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/test.cpp @@ -10012,10 +10048,10 @@ make[2]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_auto_test -O--sourcedirectory=assembler/src -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j20 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu @@ -10175,41 +10211,41 @@ 1: [ OK ] Binary.Containers (0 ms) 1: [ RUN ] Binary.Variadic 1: [ OK ] Binary.Variadic (0 ms) -1: [----------] 3 tests from Binary (1 ms total) +1: [----------] 3 tests from Binary (0 ms total) 1: 1: [----------] Global test environment tear-down -1: [==========] 58 tests from 7 test suites ran. (1 ms total) +1: [==========] 58 tests from 7 test suites ran. (0 ms total) 1: [ PASSED ] 58 tests. -1/2 Test #1: include_test ..................... Passed 0.06 sec +1/2 Test #1: include_test ..................... Passed 0.00 sec 2: Running main() from gtest_main.cpp 2: [==========] Running 98 tests from 10 test suites. 2: [----------] Global test environment set-up. 2: [----------] 6 tests from GraphCore 2: [ RUN ] GraphCore.Empty -2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.031 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.Empty (54 ms) +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.Empty (0 ms) 2: [ RUN ] GraphCore.OneVertex -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneVertex (0 ms) 2: [ RUN ] GraphCore.OneEdge -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneEdge (0 ms) 2: [ RUN ] GraphCore.VertexMethods -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.VertexMethods (0 ms) 2: [ RUN ] GraphCore.SmartIterator -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.SmartIterator (1 ms) +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.SmartIterator (0 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.054 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SelfRCEdgeMerge (0 ms) -2: [----------] 6 tests from GraphCore (55 ms total) +2: [----------] 6 tests from GraphCore (0 ms total) 2: 2: [----------] 1 test from Histogram 2: [ RUN ] Histogram.StrongWeakPtrBasic @@ -10218,7 +10254,7 @@ 2: 2: [----------] 13 tests from PairedInfo 2: [ RUN ] PairedInfo.Construct -2: [ OK ] PairedInfo.Construct (0 ms) +2: [ OK ] PairedInfo.Construct (1 ms) 2: [ RUN ] PairedInfo.Access 2: [ OK ] PairedInfo.Access (0 ms) 2: [ RUN ] PairedInfo.HalfAccess @@ -10242,10 +10278,10 @@ 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry -2: 0:00:00.055 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.055 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] PairedInfo.RandomSymmetry (230 ms) -2: [----------] 13 tests from PairedInfo (230 ms total) +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] PairedInfo.RandomSymmetry (36 ms) +2: [----------] 13 tests from PairedInfo (37 ms total) 2: 2: [----------] 13 tests from OverlapAnalysis 2: [ RUN ] OverlapAnalysis.Trivial @@ -10253,7 +10289,7 @@ 2: [ OK ] OverlapAnalysis.Trivial (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. -2: [ OK ] OverlapAnalysis.Mismatch (1 ms) +2: [ OK ] OverlapAnalysis.Mismatch (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch2 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Mismatch2 (0 ms) @@ -10284,858 +10320,858 @@ 2: [ OK ] OverlapAnalysis.SimpleGap (0 ms) 2: [ RUN ] OverlapAnalysis.UndefinedBehavior 2: [ OK ] OverlapAnalysis.UndefinedBehavior (0 ms) -2: [----------] 13 tests from OverlapAnalysis (1 ms total) +2: [----------] 13 tests from OverlapAnalysis (0 ms total) 2: 2: [----------] 17 tests from Simplification 2: [ RUN ] Simplification.SimpleTipClipperTest -2: 0:00:00.294 1M / 9M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.306 1M / 9M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.320 1M / 9M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp -2: 0:00:00.330 1M / 9M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started -2: 0:00:00.345 1M / 13M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip -2: [ OK ] Simplification.SimpleTipClipperTest (105 ms) +2: 0:00:00.037 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.037 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.038 1M / 9M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp +2: 0:00:00.038 1M / 9M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started +2: 0:00:00.039 1M / 13M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip +2: [ OK ] Simplification.SimpleTipClipperTest (3 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest -2: 0:00:00.391 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.414 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.438 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:00.451 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.475 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.486 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance -2: [ OK ] Simplification.SimpleBulgeRemovalTest (144 ms) +2: 0:00:00.039 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.039 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.040 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:00.040 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.040 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.040 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance +2: [ OK ] Simplification.SimpleBulgeRemovalTest (1 ms) 2: [ RUN ] Simplification.TipobulgeTest -2: 0:00:00.535 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.570 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.594 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:00.630 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:00.650 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:00.698 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance -2: [ OK ] Simplification.TipobulgeTest (190 ms) +2: 0:00:00.041 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.041 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.041 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:00.041 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:00.041 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.041 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance +2: [ OK ] Simplification.TipobulgeTest (0 ms) 2: [ RUN ] Simplification.SimpleECTest -2: 0:00:00.725 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.725 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.725 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.725 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.928 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleECTest (286 ms) +2: 0:00:00.041 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.041 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.041 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.041 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.062 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleECTest (37 ms) 2: [ RUN ] Simplification.SimpleIterECTest -2: 0:00:01.011 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.022 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.050 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:01.076 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:01.269 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleIterECTest (338 ms) +2: 0:00:00.078 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.078 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.078 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.078 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.094 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleIterECTest (32 ms) 2: [ RUN ] Simplification.IterECTest -2: 0:00:01.349 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.370 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.382 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:01.410 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:01.648 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.IterECTest (429 ms) +2: 0:00:00.110 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.110 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.110 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.110 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.127 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.IterECTest (33 ms) 2: [ RUN ] Simplification.IterUniquePath -2: 0:00:01.779 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.794 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.810 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:01.826 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:02.032 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: 0:00:02.050 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: 0:00:02.115 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: [ OK ] Simplification.IterUniquePath (446 ms) +2: 0:00:00.143 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.143 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.143 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.143 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.160 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: 0:00:00.160 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: 0:00:00.168 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: [ OK ] Simplification.IterUniquePath (40 ms) 2: [ RUN ] Simplification.MFUniquePath -2: 0:00:02.224 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.238 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.254 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp -2: 0:00:02.270 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started -2: 0:00:02.506 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path -2: 0:00:02.522 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy -2: [ OK ] Simplification.MFUniquePath (529 ms) +2: 0:00:00.183 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.183 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.183 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp +2: 0:00:00.183 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started +2: 0:00:00.195 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path +2: 0:00:00.195 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy +2: [ OK ] Simplification.MFUniquePath (43 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge -2: 0:00:02.753 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.774 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.786 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:02.810 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:02.835 1M / 61M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:02.883 1M / 61M INFO General (simplification_test.cpp : 276) Done -2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (153 ms) +2: 0:00:00.226 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.226 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.226 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:00.226 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.226 1M / 61M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.227 1M / 61M INFO General (simplification_test.cpp : 276) Done +2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (1 ms) 2: [ RUN ] Simplification.ComplexBulge -2: 0:00:02.907 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.930 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.954 1M / 61M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.978 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:03.002 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:03.170 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:03.194 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:03.365 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:03.842 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). -2: 0:00:03.866 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:03.967 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:03.994 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: [ OK ] Simplification.ComplexBulge (1287 ms) +2: 0:00:00.227 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.227 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.227 1M / 61M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.227 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:00.227 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.243 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:00.243 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:00.269 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.324 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). +2: 0:00:00.324 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.351 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.351 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: [ OK ] Simplification.ComplexBulge (153 ms) 2: [ RUN ] Simplification.BigComplexBulge -2: 0:00:04.194 1M / 63M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.210 1M / 63M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.230 1M / 63M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:04.259 1M / 63M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp -2: 0:00:04.290 1M / 63M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:05.370 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge -2: 0:00:05.390 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) -2: 0:00:05.559 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:06.562 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). -2: 0:00:06.586 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:06.817 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:06.850 1161M / 1161M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge -2: [ OK ] Simplification.BigComplexBulge (2882 ms) +2: 0:00:00.380 1M / 64M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.380 1M / 64M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.380 1M / 64M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.380 1M / 64M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp +2: 0:00:00.380 1M / 64M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:00.476 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge +2: 0:00:00.476 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) +2: 0:00:00.494 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.518 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). +2: 0:00:00.518 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.544 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:00.544 1161M / 1161M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge +2: [ OK ] Simplification.BigComplexBulge (193 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover -2: 0:00:07.076 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:07.090 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:07.122 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:07.154 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp -2: 0:00:07.187 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:07.228 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:07.247 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) -2: 0:00:07.322 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:07.570 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). -2: 0:00:07.603 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:07.834 2M / 154M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:07.872 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:07.915 2M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover (1472 ms) +2: 0:00:00.573 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.573 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.573 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.573 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp +2: 0:00:00.573 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:00.574 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:00.574 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) +2: 0:00:00.579 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.609 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). +2: 0:00:00.610 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.620 2M / 154M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:00.620 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:00.620 2M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover (87 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 -2: 0:00:08.548 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:08.554 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:08.578 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:08.619 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:08.636 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:08.729 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:08.742 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:08.821 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:09.025 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). -2: 0:00:09.054 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:09.152 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:09.170 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:09.194 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover1 (825 ms) +2: 0:00:00.660 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.660 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.660 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.660 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:00.660 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.676 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:00.676 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:00.702 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.757 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). +2: 0:00:00.757 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.784 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.784 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:00.784 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover1 (152 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 -2: 0:00:09.373 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:09.390 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:09.406 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:09.431 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp -2: 0:00:09.442 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started -2: 0:00:09.455 3M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:09.458 3M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) -2: 0:00:09.459 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:09.462 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). -2: 0:00:09.474 3M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:09.506 3M / 154M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:09.530 3M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:09.566 3M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover2 (288 ms) +2: 0:00:00.811 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.811 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.811 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.811 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp +2: 0:00:00.811 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started +2: 0:00:00.812 3M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:00.812 3M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) +2: 0:00:00.812 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.814 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). +2: 0:00:00.814 3M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.814 3M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:00.814 3M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:00.814 3M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover2 (11 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 -2: 0:00:09.661 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:09.670 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:09.706 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:09.734 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:09.771 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:09.818 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:09.867 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) -2: 0:00:09.918 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:09.962 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). -2: 0:00:09.986 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:10.030 1M / 154M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:10.046 1M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:10.080 1M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover3 (467 ms) +2: 0:00:00.823 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.823 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.823 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.823 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:00.823 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:00.823 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.823 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) +2: 0:00:00.823 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.823 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). +2: 0:00:00.823 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.824 1M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:00.824 1M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.824 1M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover3 (2 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 -2: 0:00:10.129 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:10.150 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:10.174 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:10.186 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp -2: 0:00:10.210 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started -2: 0:00:10.254 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:10.276 4M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) -2: 0:00:10.322 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:10.394 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). -2: 0:00:10.442 4M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:10.494 4M / 154M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:10.542 4M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:10.582 4M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover4 (621 ms) +2: 0:00:00.825 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.825 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.825 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.825 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp +2: 0:00:00.825 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started +2: 0:00:00.825 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:00.825 4M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) +2: 0:00:00.826 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.831 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). +2: 0:00:00.831 4M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.832 4M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:00.832 4M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:00.832 4M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover4 (20 ms) 2: [ RUN ] Simplification.CompressorTest -2: 0:00:10.750 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:10.770 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:10.794 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:10.819 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp -2: 0:00:10.842 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started -2: 0:00:10.867 2M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: 0:00:10.891 2M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) -2: 0:00:10.918 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:10.966 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). -2: 0:00:10.994 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:11.058 2M / 154M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:11.090 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: [ OK ] Simplification.CompressorTest (417 ms) -2: [----------] 17 tests from Simplification (10881 ms total) +2: 0:00:00.845 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.845 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.845 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.845 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp +2: 0:00:00.845 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started +2: 0:00:00.845 2M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: 0:00:00.845 2M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) +2: 0:00:00.846 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.846 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). +2: 0:00:00.846 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.846 2M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:00.846 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: [ OK ] Simplification.CompressorTest (2 ms) +2: [----------] 17 tests from Simplification (810 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread -2: 0:00:11.168 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:11.182 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:11.214 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:11.250 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:11.283 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:11.334 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:11.350 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:11.478 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 2 reads -2: 0:00:11.506 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:11.541 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:11.571 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:11.586 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:11.603 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:11.654 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:11.706 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:11.819 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. -2: 0:00:11.819 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:11.831 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. -2: 0:00:11.842 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:11.868 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). -2: 0:00:11.882 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:11.884 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:11.885 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:11.885 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:11.885 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:11.885 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:11.885 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:11.885 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:11.885 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:11.885 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:11.886 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:11.886 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:11.886 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:11.886 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread (728 ms) +2: 0:00:00.847 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.847 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.847 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.847 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.847 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.847 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.847 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.853 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 2 reads +2: 0:00:00.853 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.856 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:00.856 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.856 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.856 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.856 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.856 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.858 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. +2: 0:00:00.858 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.860 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. +2: 0:00:00.861 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.862 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). +2: 0:00:00.862 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.862 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.862 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.863 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.863 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.863 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:00.863 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.863 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.863 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:00.863 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.863 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.863 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.863 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:00.863 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread (17 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 -2: 0:00:11.896 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:11.902 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:11.927 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:11.954 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:11.979 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:12.014 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:12.050 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:12.208 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:12.208 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:12.222 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. -2: 0:00:12.239 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:12.250 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:12.275 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:12.322 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:12.338 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:12.398 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. -2: 0:00:12.406 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:12.434 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. -2: 0:00:12.446 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:12.449 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). -2: 0:00:12.449 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:12.458 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:12.467 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:12.483 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:12.499 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:12.526 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:12.562 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:12.590 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:12.600 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:12.600 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:12.601 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:12.601 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:12.601 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:12.601 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread2 (706 ms) +2: 0:00:00.864 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.864 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.864 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.864 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.864 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.864 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.864 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.868 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:00.868 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.871 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. +2: 0:00:00.871 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.871 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.871 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.871 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.871 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.875 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. +2: 0:00:00.875 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.878 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. +2: 0:00:00.878 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.878 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). +2: 0:00:00.878 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.880 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.880 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.880 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.880 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.880 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:00.881 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.881 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.881 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:00.881 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.881 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.881 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.881 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:00.881 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread2 (18 ms) 2: [ RUN ] GraphConstruction.SplitThread -2: 0:00:12.602 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:12.602 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:12.607 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:12.622 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:12.635 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:12.678 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:12.694 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:12.766 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:12.782 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:12.801 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:12.811 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:12.822 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:12.835 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:12.835 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:12.835 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:12.890 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:12.902 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:12.935 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:12.954 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:12.976 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:13.002 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:13.020 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:13.039 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:13.063 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:13.090 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:13.138 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:13.170 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:13.222 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:13.235 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:13.261 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:13.294 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:13.322 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:13.334 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:13.350 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread (782 ms) +2: 0:00:00.882 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.882 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.882 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.882 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.882 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.882 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.882 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.886 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:00.886 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.888 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:00.888 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.888 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.889 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.889 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.889 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.892 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:00.892 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.895 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:00.895 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.896 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:00.896 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.897 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.897 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.898 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.898 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.898 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:00.898 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.898 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.898 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:00.898 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.898 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.898 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.898 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:00.898 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread (17 ms) 2: [ RUN ] GraphConstruction.SplitThread2 -2: 0:00:13.384 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:13.410 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:13.423 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:13.442 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:13.450 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:13.486 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:13.506 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:13.538 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:13.554 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:13.573 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:13.587 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:13.606 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:13.619 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:13.646 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:13.662 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:13.699 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:13.714 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:13.733 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:13.758 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:13.780 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). -2: 0:00:13.794 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:13.808 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:13.827 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:13.843 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:13.859 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:13.890 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted -2: 0:00:13.918 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:13.946 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:13.963 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create -2: 0:00:13.982 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:14.014 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:14.022 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:14.038 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:14.070 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread2 (716 ms) +2: 0:00:00.899 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.899 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.899 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.899 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.899 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.899 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.899 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.901 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:00.901 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.903 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:00.903 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.903 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.904 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.904 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.904 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.907 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:00.908 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.910 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:00.910 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.911 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). +2: 0:00:00.911 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.912 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.913 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.913 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.914 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.914 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted +2: 0:00:00.914 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.914 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.914 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create +2: 0:00:00.914 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.914 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.914 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.914 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:00.914 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread2 (16 ms) 2: [ RUN ] GraphConstruction.Buldge -2: 0:00:14.100 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:14.114 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:14.131 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:14.142 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:14.158 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:14.158 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:14.158 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:14.161 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:14.162 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:14.173 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:14.187 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:14.198 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:14.211 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:14.250 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:14.266 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:14.295 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. -2: 0:00:14.310 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:14.328 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:14.342 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:14.359 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:14.374 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:14.376 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:14.376 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:14.377 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:14.377 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:14.377 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted -2: 0:00:14.377 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:14.377 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:14.377 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create -2: 0:00:14.377 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:14.377 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:14.377 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:14.377 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:14.377 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.Buldge (287 ms) +2: 0:00:00.914 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.914 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.914 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.914 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.915 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.915 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.915 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.917 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:00.917 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.920 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:00.920 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.920 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.920 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.920 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.920 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.923 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. +2: 0:00:00.923 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.926 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:00.926 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.927 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:00.927 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.929 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.929 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.929 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.929 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.929 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted +2: 0:00:00.929 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.929 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create +2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.Buldge (15 ms) 2: [ RUN ] GraphConstruction.CondenseSimple -2: 0:00:14.387 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:14.398 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:14.403 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:14.422 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:14.443 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:14.474 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:14.502 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:14.523 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:14.538 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:14.557 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:14.557 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:14.557 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:14.557 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:14.557 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:14.557 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:14.567 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:14.582 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:14.601 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:14.618 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:14.632 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:14.650 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:14.664 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:14.675 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:14.691 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:14.702 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:14.742 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:14.766 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:14.798 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:14.814 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:14.826 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:14.842 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:14.842 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:14.842 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:14.842 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.CondenseSimple (457 ms) +2: 0:00:00.930 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.930 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.930 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.930 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.930 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.930 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.930 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.932 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:00.932 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.935 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.935 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.935 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.935 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.935 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.935 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.939 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:00.939 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.942 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.942 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.943 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:00.943 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.945 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.945 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.945 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.945 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.945 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:00.945 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.945 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.945 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:00.945 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.945 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.945 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.945 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:00.945 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.CondenseSimple (16 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex -2: 0:00:14.844 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:14.844 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:14.844 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:14.844 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:14.844 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:14.844 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:14.844 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:14.844 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:14.870 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:14.874 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:14.889 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:14.889 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:14.889 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:14.889 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:14.889 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:14.889 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:14.903 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:14.920 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:14.933 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:14.950 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:14.964 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:14.978 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:14.980 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:14.980 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:14.981 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:14.981 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:14.981 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:14.981 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:14.981 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:14.981 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:14.981 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:14.981 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:14.981 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:14.981 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:14.981 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:14.981 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:14.981 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:14.981 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:14.981 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:14.982 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerStoringIndex (141 ms) +2: 0:00:00.946 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.946 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.946 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.946 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.946 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.947 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.947 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.947 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.949 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:00.949 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.952 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.952 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.952 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.952 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.952 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.952 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.955 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:00.955 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.958 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.958 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.958 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:00.958 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.960 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.960 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.961 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.961 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.961 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:00.961 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.961 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.961 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:00.961 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.961 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.961 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.961 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:00.961 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:00.961 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:00.961 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:00.961 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.961 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:00.961 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerStoringIndex (16 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex -2: 0:00:14.985 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:14.994 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:15.010 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:15.027 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:15.046 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:15.062 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:15.102 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:15.114 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:15.147 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:15.147 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:15.150 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:15.158 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:15.170 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:15.191 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:15.226 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:15.250 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:15.282 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:15.294 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:15.320 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:15.326 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:15.363 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:15.382 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:15.396 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:15.407 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:15.442 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:15.451 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:15.494 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:15.554 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:15.578 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:15.578 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:15.578 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:15.578 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:15.578 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:15.579 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:15.579 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:15.579 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:15.579 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:15.579 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:15.579 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:15.579 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerFreeIndex (595 ms) +2: 0:00:00.962 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.962 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.962 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.962 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.962 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.962 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.962 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.962 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.966 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:00.966 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.969 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.969 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.969 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.969 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.969 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.969 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.972 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:00.972 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.974 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.974 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.975 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:00.975 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.975 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.976 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.976 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.976 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.976 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:00.976 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.976 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.976 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:00.976 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.976 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.976 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.976 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:00.976 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:00.976 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:00.976 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:00.976 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.976 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:00.976 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerFreeIndex (15 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo -2: 0:00:15.580 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:15.580 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:15.580 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:15.580 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 -2: 0:00:15.580 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:15.580 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:15.580 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:15.580 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:15.686 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:15.702 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:15.720 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. -2: 0:00:15.734 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:15.758 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:15.778 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:15.806 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:15.826 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:15.958 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. -2: 0:00:15.974 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:15.988 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:15.998 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:16.019 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). -2: 0:00:16.046 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:16.064 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:16.076 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:16.102 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:16.126 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:16.158 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted -2: 0:00:16.186 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:16.214 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:16.230 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create -2: 0:00:16.250 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:16.294 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:16.306 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:16.322 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create -2: 0:00:16.350 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:16.386 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:16.406 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) -2: 0:00:16.422 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:16.422 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). -2: 0:00:16.422 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:16.422 1M / 154M INFO General (graph_construction.hpp : 93) Filling coverage index -2: 0:00:16.422 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:16.423 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). -2: 0:00:16.423 1M / 154M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. -2: 0:00:16.423 1M / 154M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM -2: 0:00:16.424 1M / 154M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process -2: 0:00:16.424 1M / 154M INFO General (graph_pack.cpp : 79) Normalizing done -2: 0:00:16.487 10M / 154M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed -2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (952 ms) -2: [----------] 9 tests from GraphConstruction (5364 ms total) +2: 0:00:00.977 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.977 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.977 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.977 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 +2: 0:00:00.977 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.977 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.978 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.978 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.982 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:00.982 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.985 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. +2: 0:00:00.985 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.985 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.985 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.986 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.986 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.989 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. +2: 0:00:00.989 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.991 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:00.991 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.992 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). +2: 0:00:00.992 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.993 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.993 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.993 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.993 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.993 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted +2: 0:00:00.994 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.994 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.994 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create +2: 0:00:00.994 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.994 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.994 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.994 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create +2: 0:00:00.994 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:00.994 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:00.994 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) +2: 0:00:00.994 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.994 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). +2: 0:00:00.994 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.994 1M / 154M INFO General (graph_construction.hpp : 93) Filling coverage index +2: 0:00:00.994 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.995 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). +2: 0:00:00.995 1M / 154M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. +2: 0:00:00.995 1M / 154M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM +2: 0:00:00.995 1M / 154M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process +2: 0:00:00.995 1M / 154M INFO General (graph_pack.cpp : 79) Normalizing done +2: 0:00:00.999 10M / 154M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed +2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (25 ms) +2: [----------] 9 tests from GraphConstruction (155 ms total) 2: 2: [----------] 3 tests from Io 2: [ RUN ] Io.Order -2: 0:00:16.532 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.554 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.760 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.766 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] Io.Order (251 ms) +2: 0:00:01.002 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.002 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.037 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.037 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] Io.Order (36 ms) 2: [ RUN ] Io.PairedInfo -2: [ OK ] Io.PairedInfo (24 ms) +2: [ OK ] Io.PairedInfo (3 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (1 ms) -2: [----------] 3 tests from Io (276 ms total) +2: [----------] 3 tests from Io (40 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor -2: 0:00:16.808 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.822 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.830 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.842 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.871 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathConstructor (72 ms) +2: 0:00:01.042 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.042 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.042 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.042 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.042 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathConstructor (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove -2: 0:00:16.880 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.894 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.914 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.942 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.954 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemove (90 ms) +2: 0:00:01.042 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.042 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.042 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.042 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.042 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemove (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps -2: 0:00:16.970 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.970 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.970 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.970 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.971 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.042 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.042 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.042 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.042 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathEquals -2: 0:00:16.971 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.971 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.971 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.971 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.971 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathEquals (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSubpaths -2: 0:00:16.971 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.971 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.971 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.971 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.972 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSubpaths (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveConjugate -2: 0:00:16.972 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.972 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.972 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.972 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.972 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSearch -2: 0:00:16.972 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.972 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.972 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.972 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.972 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathSearch (1 ms) +2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathSearch (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathLoopDetector -2: 0:00:16.972 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.972 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.972 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.972 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.973 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathLoopDetector (0 ms) -2: [----------] 8 tests from PathExtend (165 ms total) +2: [----------] 8 tests from PathExtend (2 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff -2: 0:00:16.973 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.973 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.973 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.973 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.973 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] OverlapRemoval.BasicNoDiff (0 ms) +2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] OverlapRemoval.BasicNoDiff (1 ms) 2: [ RUN ] OverlapRemoval.BasicDiff -2: 0:00:16.973 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.973 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.973 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.973 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.974 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] OverlapRemoval.BasicDiff (1 ms) +2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] OverlapRemoval.BasicDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatConjugateEdges -2: 0:00:16.974 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:16.974 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:16.974 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:16.979 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:16.986 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: 0:00:17.002 1M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (45 ms) +2: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.045 1M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat -2: 0:00:17.019 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.034 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.054 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.078 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.107 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:17.111 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeat (108 ms) +2: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.050 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.050 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeat (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven -2: 0:00:17.126 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.158 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.174 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.190 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.219 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:17.230 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatUneven (119 ms) +2: 0:00:01.050 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.050 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.050 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.050 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.054 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.055 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatUneven (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected -2: 0:00:17.246 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.266 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.282 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.298 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.322 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:17.330 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:17.330 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (85 ms) +2: 0:00:01.055 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.055 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.055 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.055 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.059 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.059 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.059 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect -2: 0:00:17.331 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.331 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.331 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.331 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.344 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:17.346 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (31 ms) +2: 0:00:01.059 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.059 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.064 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.064 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd -2: 0:00:17.362 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.378 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.394 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.410 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.434 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:17.442 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:17.461 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEnd (99 ms) +2: 0:00:01.064 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.064 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.064 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.064 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.068 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.068 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.068 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEnd (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain -2: 0:00:17.461 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.461 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.461 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.461 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.473 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:17.474 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:17.491 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (45 ms) +2: 0:00:01.069 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.069 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.069 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.069 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.073 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.073 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.073 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart -2: 0:00:17.506 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.525 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.538 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.538 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.547 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:17.557 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:17.570 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStart (83 ms) +2: 0:00:01.073 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.073 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.073 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.073 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.078 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.078 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.078 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStart (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain -2: 0:00:17.589 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.602 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.621 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.635 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.658 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:17.666 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:17.666 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (78 ms) +2: 0:00:01.078 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.078 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.078 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.078 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.082 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.082 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.082 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (5 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication -2: 0:00:17.666 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.667 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.667 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.667 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.675 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplication (16 ms) +2: 0:00:01.083 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.083 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.083 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.083 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.087 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplication (4 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual -2: 0:00:17.683 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.698 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.714 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.715 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.726 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (52 ms) +2: 0:00:01.087 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.087 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.087 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.087 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.092 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (5 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff -2: 0:00:17.735 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.735 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.735 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.735 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.743 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiff (20 ms) +2: 0:00:01.092 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.092 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.092 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.092 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.096 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiff (5 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap -2: 0:00:17.755 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.774 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.794 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.814 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.842 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiffGap (100 ms) +2: 0:00:01.096 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.096 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.096 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.096 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.101 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiffGap (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 -2: 0:00:17.854 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.874 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.874 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.874 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.882 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (40 ms) +2: 0:00:01.101 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.101 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.101 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.101 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.105 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (5 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 -2: 0:00:17.895 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.914 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.934 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.954 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:17.982 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (100 ms) +2: 0:00:01.106 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.106 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.106 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.106 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.110 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (4 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen -2: 0:00:17.994 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:17.995 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:17.995 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:17.995 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:18.002 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:18.014 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:18.038 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (67 ms) +2: 0:00:01.110 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.110 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.110 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.110 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.115 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.115 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.115 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (5 ms) 2: [ RUN ] OverlapRemoval.Tricky0 -2: 0:00:18.062 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:18.074 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:18.102 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:18.114 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:18.145 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:18.158 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:18.174 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky0 (139 ms) +2: 0:00:01.115 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.115 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.115 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.115 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.119 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.119 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.119 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky0 (5 ms) 2: [ RUN ] OverlapRemoval.Tricky1 -2: 0:00:18.202 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:18.214 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:18.214 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:18.214 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:18.230 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:18.242 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:18.262 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky1 (87 ms) +2: 0:00:01.119 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.119 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.119 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.119 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.124 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.124 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.124 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky1 (4 ms) 2: [ RUN ] OverlapRemoval.Tricky2 -2: 0:00:18.290 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:18.302 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:18.314 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:18.314 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:18.326 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:18.334 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:18.358 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky2 (84 ms) +2: 0:00:01.124 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.124 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.124 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.124 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.128 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.129 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.129 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky2 (5 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen -2: 0:00:18.374 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:18.394 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:18.414 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:18.442 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:18.470 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:18.486 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:18.506 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicMinEdgeLen (152 ms) +2: 0:00:01.129 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.129 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.129 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.129 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.133 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.133 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.133 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicMinEdgeLen (5 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle -2: 0:00:18.526 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:18.542 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:18.570 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:18.586 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:18.609 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:18.622 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:18.638 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.OverlapWithMiddle (128 ms) -2: [----------] 23 tests from OverlapRemoval (1682 ms total) +2: 0:00:01.133 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.133 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.133 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.133 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.138 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.138 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.138 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.OverlapWithMiddle (4 ms) +2: [----------] 23 tests from OverlapRemoval (94 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest -2: 0:00:18.655 1M / 154M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 -2: [ OK ] GraphAligner.EdlibSHWFULLTest (15 ms) +2: 0:00:01.138 1M / 154M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 +2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero -2: 0:00:18.670 1M / 154M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 -2: 0:00:18.690 1M / 154M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 -2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (44 ms) +2: 0:00:01.138 1M / 154M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 +2: 0:00:01.138 1M / 154M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 +2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest -2: 0:00:18.714 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:18.726 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:18.740 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:18.758 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:18.794 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:18.818 5M / 154M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm -2: [ OK ] GraphAligner.TrivialTest (2349 ms) +2: 0:00:01.138 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.138 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.138 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.138 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.143 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.150 5M / 154M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm +2: [ OK ] GraphAligner.TrivialTest (409 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest -2: 0:00:21.063 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:21.086 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:21.106 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:21.138 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:21.174 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraOneEdgeTest (128 ms) +2: 0:00:01.547 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.547 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.547 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.547 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.551 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraOneEdgeTest (5 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest -2: 0:00:21.191 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:21.206 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:21.222 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:21.238 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:21.293 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraGrowEndsTest (116 ms) -2: [----------] 5 tests from GraphAligner (2652 ms total) +2: 0:00:01.552 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.552 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.552 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.552 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.556 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraGrowEndsTest (5 ms) +2: [----------] 5 tests from GraphAligner (419 ms total) 2: 2: [----------] Global test environment tear-down -2: [==========] 98 tests from 10 test suites ran. (21307 ms total) +2: [==========] 98 tests from 10 test suites ran. (1557 ms total) 2: [ PASSED ] 98 tests. -2/2 Test #2: debruijn_test .................... Passed 21.37 sec +2/2 Test #2: debruijn_test .................... Passed 1.56 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 21.81 sec +Total Test time (real) = 1.57 sec make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_prep -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_auto_install --destdir=debian/spades/ -O--sourcedirectory=assembler/src -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/spades-3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/spades-3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -11157,28 +11193,28 @@ -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades_init.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/VERSION -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.gff --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.txt -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.txt +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.gff +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.gff +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R2.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R1.fastq.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R1.fastq.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R2.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R2.fastq.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R1.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KS.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KS.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms/Phan-CoV.hmm.gz @@ -11190,27 +11226,27 @@ -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/GPLv2.txt -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-core -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/tsa.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/construction.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/simplification.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/config.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/moleculo_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/tsa.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/simplification.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/pe_params.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/construction.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/moleculo_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/config.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/toy.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-hammer -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/hammer -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/hammer/config.info @@ -11241,49 +11277,49 @@ -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/options_parser.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/compress_all.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/plasmid_glue.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/correction_iteration_script.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_interlaced_reads.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/check_test_script.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_contigs.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/breaking_scaffolds_script.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/postprocessing_script.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/plasmid_glue.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/copy_files.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/check_test_script.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_interlaced_reads.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/postprocessing_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/check_test_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/terminating_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/breaking_scaffolds_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/before_start_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/postprocessing_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/preprocess_reads_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/check_test_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/error_correction_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/__init__.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/pipeline.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_iteration_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/error_correction_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/breaking_scaffolds_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/correction_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/terminating_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/pipeline.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/break_by_coverage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_postprocessing.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/reference_construction.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/string_dist_utils.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_filter_contigs.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/id_generation.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/launch_options.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/__init__.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/barcode_extraction.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/reference_construction.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/id_generation.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/break_by_coverage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/generate_quality.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_postprocessing.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/launch_options.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/string_dist_utils.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/barcode_extraction.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/alignment.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/parallel_launcher.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/__init__.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/SeqIO.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/sam_parser.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/SeqIO.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/__init__.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/alignment.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executors.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_save_yaml.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_local.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executors.py make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' @@ -11339,12 +11375,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3654805/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3654805/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1769919 and its subdirectories -I: Current time: Mon Dec 16 11:23:43 -12 2024 -I: pbuilder-time-stamp: 1734391423 +I: removing directory /srv/workspace/pbuilder/3654805 and its subdirectories +I: Current time: Mon Jan 19 19:54:41 +14 2026 +I: pbuilder-time-stamp: 1768802081