Diff of the two buildlogs: -- --- b1/build.log 2025-10-23 05:19:58.994042958 +0000 +++ b2/build.log 2025-10-23 05:32:51.734915739 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Oct 22 17:09:42 -12 2025 -I: pbuilder-time-stamp: 1761196182 +I: Current time: Thu Nov 26 01:43:02 +14 2026 +I: pbuilder-time-stamp: 1795606982 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -44,52 +44,84 @@ dpkg-source: info: applying gcc-15.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/418759/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/741642/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 Nov 25 11:43 /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/741642/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/741642/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=12 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=16 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a807e8a741b74595a7aa59c5fd089f9a' - 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='418759' - PS1='# ' - PS2='> ' + INVOCATION_ID=e27449820a984c188cf3a27f43c4e6ab + 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=741642 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.hAxOg6fT/pbuilderrc_P4UD --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hAxOg6fT/b1 --logfile b1/build.log spades_4.0.0+really3.15.5+dfsg-3.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.hAxOg6fT/pbuilderrc_Bmbr --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hAxOg6fT/b2 --logfile b2/build.log spades_4.0.0+really3.15.5+dfsg-3.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.48+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/418759/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/741642/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -360,7 +392,7 @@ Get: 187 http://deb.debian.org/debian forky/main amd64 lynx amd64 2.9.2-1 [641 kB] Get: 188 http://deb.debian.org/debian forky/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get: 189 http://deb.debian.org/debian forky/main amd64 python3-joblib all 1.4.2-5 [216 kB] -Fetched 201 MB in 9s (23.1 MB/s) +Fetched 201 MB in 6s (31.8 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19898 files and directories currently installed.) @@ -974,8 +1006,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Oct 23 05:13:17 UTC 2025. -Universal Time is now: Thu Oct 23 05:13:17 UTC 2025. +Local time is now: Wed Nov 25 11:47:39 UTC 2026. +Universal Time is now: Wed Nov 25 11:47:39 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -1151,7 +1183,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/spades-4.0.0+really3.15.5+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_4.0.0+really3.15.5+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/741642/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/741642/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/spades-4.0.0+really3.15.5+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_4.0.0+really3.15.5+dfsg-3_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 4.0.0+really3.15.5+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -1425,8 +1461,8 @@ to work with policies introduced by or earlier. --- Configuring done (12.8s) --- Generating done (0.4s) +-- Configuring done (14.7s) +-- Generating done (0.8s) CMake Warning: Manually-specified variables were not used by the project: @@ -1441,7 +1477,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg' dh_auto_build -- all debruijn_test include_test - cd obj-x86_64-linux-gnu && make -j12 INSTALL="install --strip-program=true" all debruijn_test include_test VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j16 INSTALL="install --strip-program=true" all debruijn_test include_test VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1456,93 +1492,125 @@ cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore/CMakeFiles/ConsensusCore.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+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 +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+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 -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/getopt_pp /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp/CMakeFiles/getopt_pp.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" +make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+really3.15.5+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 make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" +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[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gfa1 /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake "--color=" -make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" -make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/CMakeFiles/easel.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/mapping_printer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/build +make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/build +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/build +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 0%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o -[ 0%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 0%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/build +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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/gfa1/CMakeFiles/gfa1.dir/gfa.c.o -MF CMakeFiles/gfa1.dir/gfa.c.o.d -o CMakeFiles/gfa1.dir/gfa.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gfa1/gfa.c -make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/edlib/CMakeFiles/edlib.dir/edlib.cpp.o -MF CMakeFiles/edlib.dir/edlib.cpp.o.d -o CMakeFiles/edlib.dir/edlib.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/edlib/edlib.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -MF CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o.d -o CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/getopt_pp/getopt_pp.cpp make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 1%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o -[ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -[ 2%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -[ 2%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 2%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf/gqf.c -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/AffineAlignment.cpp.o -MF CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o.d -o CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/AffineAlignment.cpp +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/build +[ 0%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 0%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest-all.cc -[ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 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'/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/edlib/CMakeFiles/edlib.dir/edlib.cpp.o -MF CMakeFiles/edlib.dir/edlib.cpp.o.d -o CMakeFiles/edlib.dir/edlib.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/edlib/edlib.cpp +[ 1%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o +[ 1%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o +[ 1%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o +[ 1%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o +[ 1%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o +[ 1%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o +[ 1%] Building C object ext/easel/CMakeFiles/easel.dir/easel.c.o +[ 1%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/c++ -DNDEBUG 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/getopt_pp/getopt_pp.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wall -Wextra -pedantic -Wno-deprecated -O2 -MD -MT ext/cppformat/CMakeFiles/format.dir/format.cc.o -MF CMakeFiles/format.dir/format.cc.o.d -o CMakeFiles/format.dir/format.cc.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat/format.cc -[ 2%] Building C object ext/easel/CMakeFiles/easel.dir/easel.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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/easel.c.o -MF CMakeFiles/easel.dir/easel.c.o.d -o CMakeFiles/easel.dir/easel.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/easel.c +[ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary -isystem 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-o CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/AffineAlignment.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -fPIC -Wno-deprecated -O2 -Wall -Wextra -Wno-unknown-pragmas -fvisibility=hidden -Wno-invalid-memory-model -ftls-model=initial-exec -MD -MT ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -MF CMakeFiles/mimalloc-obj.dir/src/static.c.o.d -o CMakeFiles/mimalloc-obj.dir/src/static.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamAlignment.cpp.o -MF CMakeFiles/BamTools.dir/BamAlignment.cpp.o.d -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/BamAlignment.cpp +[ 1%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o +[ 1%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o +[ 2%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o +[ 2%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem 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-D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/APFloat.cpp.o -MF CMakeFiles/llvm-support.dir/APFloat.cpp.o.d -o CMakeFiles/llvm-support.dir/APFloat.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/APFloat.cpp +[ 2%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf/gqf.c +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/version.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/reproducible-path/spades-4.0.0+really3.15.5+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); @@ -1584,6 +1652,8 @@ | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} +[ 3%] Linking CXX static library libversion.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_deserialize': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:1606:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1606 | fread(qf->metadata, sizeof(qfmetadata), 1, fin); @@ -1591,6 +1661,11 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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 +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 3%] Built target version In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:28: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c: In function 'void _mi_mem_collect(mi_os_tld_t*)': /build/reproducible-path/spades-4.0.0+really3.15.5+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] @@ -1599,6 +1674,8 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c:89:16: note: 'mem_region_t' {aka 'struct mem_region_s'} declared here 89 | typedef struct mem_region_s { | ^~~~~~~~~~~~ +[ 3%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/APInt.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:31: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/heap.c: In function 'mi_heap_t* mi_heap_new()': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/heap.c:196:9: 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] @@ -1719,91 +1796,21 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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 { | ^~~~~~~~~ -[ 3%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o +[ 4%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_alphabet.c.o -MF CMakeFiles/easel.dir/esl_alphabet.c.o.d -o CMakeFiles/easel.dir/esl_alphabet.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_alphabet.c -[ 3%] Linking C static library libgqf.a +[ 4%] Linking C static library libgqf.a cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gqf.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /usr/bin/ar qc libgqf.a CMakeFiles/gqf.dir/gqf.c.o /usr/bin/ranlib libgqf.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 3%] Built target gqf -[ 3%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_avx.c -[ 3%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/BamMultiReader.cpp -[ 3%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/Coverage.cpp.o -MF CMakeFiles/ConsensusCore.dir/Coverage.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Coverage.cpp -[ 3%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_buffer.c -[ 3%] Linking CXX static library libgetopt_pp.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -E cmake_link_script CMakeFiles/getopt_pp.dir/link.txt --verbose=1 -/usr/bin/ar qc libgetopt_pp.a CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -/usr/bin/ranlib libgetopt_pp.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 3%] Built target getopt_pp -[ 3%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_cluster.c -[ 3%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/Mutation.cpp.o -MF CMakeFiles/ConsensusCore.dir/Mutation.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Mutation.cpp -[ 3%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_composition.c -[ 4%] Linking CXX static library libedlib.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 -[ 4%] Linking C static library libgfa1.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 -[ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_dirichlet.c -/usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o -/usr/bin/ranlib libedlib.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 5%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamReader.cpp.o -MF CMakeFiles/BamTools.dir/BamReader.cpp.o.d -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/BamReader.cpp -[ 5%] Built target edlib -/usr/bin/ar qc libgfa1.a CMakeFiles/gfa1.dir/gfa.c.o -/usr/bin/ranlib libgfa1.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 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-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/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/APInt.cpp -[ 5%] Built target gfa1 -[ 5%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Atomic.cpp -[ 5%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG 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CMakeFiles/format.dir/posix.cc.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat/posix.cc -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 5%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp -[ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_distance.c -[ 5%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/BamWriter.cpp -[ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_dmatrix.c -[ 5%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/genomic_info.cpp -[ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_dsqdata.c -[ 5%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamHeader.cpp -[ 6%] Linking CXX static library libformat.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 6%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/version.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9, @@ -1813,52 +1820,42 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o -/usr/bin/ranlib libformat.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 8%] Linking CXX static library libversion.a -[ 8%] Built target format -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake -[ 8%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/PairwiseAlignment.cpp.o -MF CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o.d -o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/PairwiseAlignment.cpp -[ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_exponential.c -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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_ ? - | ^~~~~~~ -/usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o -/usr/bin/ranlib libversion.a +[ 4%] Built target gqf +[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/Coverage.cpp.o -MF CMakeFiles/ConsensusCore.dir/Coverage.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Coverage.cpp +[ 4%] Linking CXX static library libgetopt_pp.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -E cmake_link_script CMakeFiles/getopt_pp.dir/link.txt --verbose=1 +[ 4%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/BamMultiReader.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp:1: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 4%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_avx.c +/usr/bin/ar qc libgetopt_pp.a CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o +/usr/bin/ranlib libgetopt_pp.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 8%] Built target version -[ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c -[ 10%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Sequence.cpp -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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++; - | ^ -[ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgram.cpp +[ 4%] Built target getopt_pp +[ 4%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_buffer.c +[ 4%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp +[ 4%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/genomic_info.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:363:10: warning: unused variable 'loaded' [-Wunused-variable] 363 | bool loaded = base::BinRead(is, gp); | ^~~~~~ +[ 5%] Linking CXX static library libedlib.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake +[ 5%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/Mutation.cpp.o -MF CMakeFiles/ConsensusCore.dir/Mutation.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Mutation.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:207:19: required from here 207 | graph_io_.Load(basename, g); @@ -1929,38 +1926,46 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] 130 | auto loaded = io.BinRead(is, component); | ^~~~~~ -[ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_gamma.c -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" +[ 5%] Linking C static library libgfa1.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 +/usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o +/usr/bin/ranlib libedlib.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 12%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_cluster.c +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Atomic.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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_ ? + | ^~~~~~~ +[ 5%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/PairwiseAlignment.cpp.o -MF CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o.d -o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/CrashRecoveryContext.cpp.o -MF CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d -o CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/CrashRecoveryContext.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgramChain.cpp -[ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_gencode.c -[ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Utils.cpp -[ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_getopts.c -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 13%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp -[ 13%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroup.cpp +[ 6%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_composition.c +[ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_dirichlet.c +[ 8%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamReader.cpp.o -MF CMakeFiles/BamTools.dir/BamReader.cpp.o.d -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/BamReader.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp:1: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { @@ -1971,88 +1976,37 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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 -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 13%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp -[ 13%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp -[ 13%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp -[ 13%] Linking CXX static library libsequence.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake -[ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp:1: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 13%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o -/usr/bin/ranlib libsequence.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 13%] Built target sequence -[ 13%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:109:33: required from here - 109 | helper.LinkEdges(e1, e2); - | ~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+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); - | ^~~ -[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_gumbel.c -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_distance.c +[ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_dmatrix.c +[ 9%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Sequence.cpp +[ 9%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/BamWriter.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -2062,62 +2016,13 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp:1: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_heap.c.o -MF CMakeFiles/easel.dir/esl_heap.c.o.d -o CMakeFiles/easel.dir/esl_heap.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_heap.c -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequenceDictionary.cpp -[ 16%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp -[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_histogram.c -[ 16%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Version.cpp -[ 16%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Debug.cpp -[ 16%] Linking CXX static library libcoverage_model.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -/usr/bin/ranlib libcoverage_model.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 16%] Built target coverage_model -[ 16%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -2125,17 +2030,53 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_hmm.c -[ 16%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Errno.cpp +[ 9%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp +[ 9%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wall -Wextra -pedantic -Wno-deprecated -O2 -MD -MT ext/cppformat/CMakeFiles/format.dir/posix.cc.o -MF CMakeFiles/format.dir/posix.cc.o.d -o CMakeFiles/format.dir/posix.cc.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat/posix.cc +[ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Debug.cpp +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" +[ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o -MF CMakeFiles/sequence.dir/sequence_tools.cpp.o.d -o CMakeFiles/sequence.dir/sequence_tools.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence/sequence_tools.cpp +[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o +cd 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c +[ 13%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o +cd 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-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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp +[ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Version.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, @@ -2145,83 +2086,56 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 16%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Matrix/DenseMatrix.cpp -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamHeader_p.cpp -[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_hyperexp.c -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_keyhash.c -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_mem.c -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 17%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Error.cpp -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_minimizer.c.o -MF CMakeFiles/easel.dir/esl_minimizer.c.o.d -o CMakeFiles/easel.dir/esl_minimizer.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_minimizer.c -make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/depend +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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++; + | ^ +[ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_gamma.c +[ 13%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Errno.cpp +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/mapping_printer.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/build +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp -[ 17%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp -[ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_mixgev.c -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_mpi.c -[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msa.c -[ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 13%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/memory_limit.cpp.o -MF CMakeFiles/utils.dir/memory_limit.cpp.o.d -o CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/memory_limit.cpp +[ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_gencode.c +[ 13%] Linking CXX static library libsequence.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 +[ 13%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroup.cpp +[ 13%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp +/usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o +/usr/bin/ranlib libsequence.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 13%] Built target sequence +[ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_getopts.c +[ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp -[ 18%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp -[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamWriter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -2229,8 +2143,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 20%] Linking CXX static library libgraphio.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake /build/reproducible-path/spades-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -2243,13 +2155,28 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -/usr/bin/ranlib libgraphio.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 20%] Built target graphio -[ 22%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/FoldingSet.cpp +[ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Matrix/DenseMatrix.cpp +[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_gumbel.c +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:109:33: required from here + 109 | helper.LinkEdges(e1, e2); + | ~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+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); + | ^~~ +[ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp +[ 15%] Linking CXX static library libcoverage_model.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 +[ 15%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Error.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -2269,46 +2196,28 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msacluster.c -[ 23%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConfig.cpp -[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile.c -[ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -[ 23%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp -[ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp -[ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp -/build/reproducible-path/spades-4.0.0+really3.15.5+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]': +/usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o +/usr/bin/ranlib libcoverage_model.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 15%] Built target coverage_model +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -2321,6 +2230,14 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp +[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_heap.c.o -MF CMakeFiles/easel.dir/esl_heap.c.o.d -o CMakeFiles/easel.dir/esl_heap.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_heap.c +[ 16%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConfig.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -2328,30 +2245,26 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, - | ^~~~~~~~~~~~~ -[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile2.c +[ 16%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp +[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_histogram.c +[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -2382,16 +2295,27 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/FormatVariadic.cpp -[ 23%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/memory_limit.cpp.o -MF CMakeFiles/utils.dir/memory_limit.cpp.o.d -o CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/memory_limit.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 16%] Linking CXX static library libmapping_printer.a +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/mapping_printer.dir/link.txt --verbose=1 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: /build/reproducible-path/spades-4.0.0+really3.15.5+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=] @@ -2414,35 +2338,38 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 23%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/PoaGraph.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaGraph.cpp -[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_a2m.c -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_afa.c -[ 24%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include 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CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp -[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Hashing.cpp -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include 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CMakeFiles/easel.dir/esl_msafile_clustal.c.o.d -o CMakeFiles/easel.dir/esl_msafile_clustal.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_clustal.c -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Host.cpp -[ 24%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp -[ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamFile_p.cpp.o -MF 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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamFile_p.cpp -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include 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-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_hmm.c +[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp +/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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 16%] Built target mapping_printer +[ 17%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/filesystem/temporary.cpp -/build/reproducible-path/spades-4.0.0+really3.15.5+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]': +[ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_keyhash.c +[ 19%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamHeader_p.cpp +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/FoldingSet.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -2461,9 +2388,36 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 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ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 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-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_mixgev.c +[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/FormatVariadic.cpp +[ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_mpi.c +[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Hashing.cpp +[ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msa.c +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -2482,152 +2436,79 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_stockholm.c -[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.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 = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, + | ^~~~~~~~~~~~~ +[ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msacluster.c +[ 22%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/filesystem/glob.cpp +[ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o +[ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/BamWriter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp +[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Host.cpp +[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/JSON.cpp +[ 23%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem 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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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp +[ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp +[ 24%] Linking CXX static library libgraphio.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 +/usr/bin/ranlib libgraphio.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 24%] Built target graphio +[ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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 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-isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/LEB128.cpp +[ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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 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ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -MF 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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamFile_p.cpp +[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile.c +[ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ 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-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp [ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ByteArray_p.cpp [ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp +[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile2.c [ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/string:45, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/binary.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/io_base.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:9: -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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: 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=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ [ 27%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp -[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msashuffle.c -[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msaweight.c -[ 29%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/filesystem/glob.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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 29%] Linking CXX static library ../../../lib/libgtest.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 -[ 29%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/logger/logger_impl.cpp -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/LEB128.cpp -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_normal.c -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_paml.c -/usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" -/usr/bin/ranlib ../../../lib/libgtest.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o +[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_a2m.c +[ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/LineIterator.cpp -[ 30%] Built target gtest -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Locale.cpp -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/MD5.cpp -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_random.c -[ 30%] Linking CXX static library libmapping_printer.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/mapping_printer.dir/link.txt --verbose=1 -[ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_afa.c +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_phylip.c +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_clustal.c +[ 29%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_psiblast.c cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp -/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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 30%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o +[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Locale.cpp +[ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c -[ 30%] Built target mapping_printer -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 30%] Linking CXX static library libpaired_info.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_randomseq.c -[ 31%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.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> >, 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: 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=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': /build/reproducible-path/spades-4.0.0+really3.15.5+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] @@ -2636,52 +2517,10 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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); | ^~~~~~~~~~ -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest_main.cc -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_ratematrix.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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/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 -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 31%] Built target paired_info -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_recorder.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_regexp.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_rootfinder.c -[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/MemAlloc.cpp -[ 33%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/MemoryBuffer.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c -[ 33%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o +[ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c -[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sq.c +[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/MD5.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /build/reproducible-path/spades-4.0.0+really3.15.5+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] @@ -2697,41 +2536,72 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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); | ^~~~~~~~ -[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sqio.c -[ 33%] Linking CXX static library ../../../lib/libgtest_main.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake -cd 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/NativeFormatting.cpp -/usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -/usr/bin/ranlib ../../../lib/libgtest_main.a -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" -[ 33%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -[ 33%] Built target gtest_main +[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o +cd 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-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_selex.c +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_stockholm.c +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/MemAlloc.cpp +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msashuffle.c +[ 31%] Linking CXX static library libpaired_info.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_msaweight.c +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 31%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/MemoryBuffer.cpp +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_normal.c +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_paml.c +[ 31%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c:23: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c: In function 'esl_scorematrix_Create': -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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__ - | ^~~~~~ -[ 33%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Path.cpp +/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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 33%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_gtest.cpp +[ 31%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/NativeFormatting.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: /build/reproducible-path/spades-4.0.0+really3.15.5+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); @@ -2743,10 +2613,17 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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); | ^~~~~~~~~~~ -[ 33%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp -[ 34%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o +[ 32%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c +[ 32%] Built target paired_info +[ 32%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Path.cpp +[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_random.c +[ 32%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: /build/reproducible-path/spades-4.0.0+really3.15.5+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); @@ -2758,12 +2635,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ascii.c -[ 34%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: /build/reproducible-path/spades-4.0.0+really3.15.5+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); @@ -2775,10 +2646,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ncbi.c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': /build/reproducible-path/spades-4.0.0+really3.15.5+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", @@ -2798,17 +2665,24 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; - | ^~~~~~~~ +[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_randomseq.c +[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_ratematrix.c +[ 33%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp +[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_recorder.c +[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Program.cpp +[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Regex.cpp +[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp [ 34%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_regexp.c In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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); @@ -2820,16 +2694,58 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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); | ^~~~~~~~~~~ -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sse.c -[ 36%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o +[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/SmallVector.cpp +[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/SourceMgr.cpp +[ 34%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_ssi.c -[ 37%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/string:45, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/binary.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/io_base.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:9: +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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: 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=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_rootfinder.c +[ 36%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_stack.c +[ 36%] Linking CXX static library libutils.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 +[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/StringExtras.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined @@ -2842,147 +2758,253 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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%] Linking CXX static library libteamcity_gtest.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake [ 37%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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 -/usr/bin/ranlib libteamcity_gtest.a +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; + | ^~~~~~~~ +[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/StringMap.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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 37%] Built target teamcity_gtest -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_stats.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_stopwatch.c -[ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Program.cpp +[ 37%] Built target utils +[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/StringRef.cpp +[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/StringSaver.cpp +[ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c +[ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sq.c +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c:23: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c: In function 'esl_scorematrix_Create': +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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__ + | ^~~~~~ +[ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/ThreadLocal.cpp [ 38%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp -[ 38%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o +[ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sqio.c +[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Threading.cpp +[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.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> >, 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: 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=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/TimeProfiler.cpp +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ascii.c +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ncbi.c +[ 39%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 39%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o +[ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_sse.c +[ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Twine.cpp +[ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Unicode.cpp +[ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o +cd 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CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/WithColor.cpp +[ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/YAMLTraits.cpp +[ 41%] Linking CXX static library ../../../lib/libgtest.a +cd 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Regex.cpp -[ 39%] Linking CXX static library libutils.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o +/usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" +/usr/bin/ranlib ../../../lib/libgtest.a +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_threads.c -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o +[ 43%] Built target gtest +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/raw_ostream.cpp make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 39%] Built target utils -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/SmallVector.cpp -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 43%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem 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-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem 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CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/StringRef.cpp -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o +[ 44%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/StringSaver.cpp -[ 43%] Linking CXX static library libBamTools.a +[ 44%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/regcomp.c +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 44%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/regerror.c +[ 44%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_gtest.cpp +[ 45%] Linking CXX static library libBamTools.a cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake -[ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/ThreadLocal.cpp -[ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/Threading.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 -[ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/TimeProfiler.cpp -[ 44%] Linking CXX static library libbinary_io.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 -[ 44%] Linking C static library libeasel.a +[ 45%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp +[ 46%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/regexec.c +[ 46%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/regfree.c +[ 46%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/regstrlcpy.c +[ 46%] Linking C static library libeasel.a cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 -[ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -cd 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CMakeFiles/easel.dir/esl_wuss.c.o -/usr/bin/ranlib libeasel.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem 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object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/raw_ostream.cpp -[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_import.c -[ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include 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CMakeFiles/hmmer.dir/src/eweight.c.o.d -o CMakeFiles/hmmer.dir/src/eweight.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/eweight.c -[ 48%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/regcomp.c -[ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer 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-ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_decoding.c.o -MF CMakeFiles/hmmer.dir/src/generic_decoding.c.o.d -o CMakeFiles/hmmer.dir/src/generic_decoding.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_decoding.c -[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /build/reproducible-path/spades-4.0.0+really3.15.5+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); @@ -3008,18 +3030,16 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -[ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_pileup.c -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem 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ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 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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/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-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_md.c -[ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/regerror.c [ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/razf.c +[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem 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'razf_flush': /build/reproducible-path/spades-4.0.0+really3.15.5+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); @@ -3061,48 +3081,57 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o +[ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/faidx.c +[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake +[ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bedidx.c +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 +[ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o +[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_sort.c +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_stotrace.c -[ 52%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/heatmap.c -[ 54%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include 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ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/kprobaln.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmlogo.c -[ 54%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_cat.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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/hmmdmstr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdmstr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o @@ -3114,174 +3143,178 @@ [ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/logsum.c [ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/modelconfig.c +[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/modelstats.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/mpisupport.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG 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-isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/seqmodel.c +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/mpisupport.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/tracealign.c -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_bg.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_bg.c cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_builder.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmx.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src 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CMakeFiles/hmmer.dir/src/p7_gmxb.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmxb.c -[ 58%] Linking CXX static library libsamtools.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmcache.c -/usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/bam_cat.c.o -/usr/bin/ranlib libsamtools.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmfile.c -[ 59%] Built target samtools +[ 59%] Linking CXX static library libbinary_io.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_ssv.c.o -MF CMakeFiles/hmmer.dir/src/fm_ssv.c.o.d -o CMakeFiles/hmmer.dir/src/fm_ssv.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_ssv.c +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o +[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o +[ 62%] Built target samtools +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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/io.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/io.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/io.c +/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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 63%] Built target binary_io +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated 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CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/msvfilter.c +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" -cd 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_prior.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: 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63%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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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CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/optacc.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c +[ 65%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/paired_readers.cpp -[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_spensemble.c -[ 60%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/vitfilter.c +[ 65%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/binary_converter.cpp -[ 61%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_omx.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_oprofile.c +[ 66%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include 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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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/io_helper.cpp -[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem 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66%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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 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common/io/CMakeFiles/input.dir/sam/read.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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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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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/sam/sam_reader.cpp -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmpgmd2msa.c -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp:9: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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_ssv.c.o -MF CMakeFiles/hmmer.dir/src/fm_ssv.c.o.d -o CMakeFiles/hmmer.dir/src/fm_ssv.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_ssv.c -[ 65%] Built target llvm-support +[ 67%] 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o +[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp -[ 66%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/fwdback.c -[ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o +[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o +[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp -[ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer 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-isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp -[ 67%] Linking CXX static library libConsensusCore.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake -[ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem 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CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/ssvfilter.c -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 -[ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/msvfilter.c -/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 -/usr/bin/ranlib libConsensusCore.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 67%] Built target ConsensusCore -[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o +[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp:5: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o +[ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp +[ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp:5: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp -make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:11, @@ -3290,11 +3323,6 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:3, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: @@ -3310,11 +3338,21 @@ | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 69%] Linking CXX static library libConsensusCore.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -3324,12 +3362,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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 C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/null2.c -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp -[ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/optacc.c In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:9: @@ -3358,36 +3390,39 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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_; | ^~~~~~~~ -[ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o +/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 +/usr/bin/ranlib libConsensusCore.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 69%] 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' [ 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/pair_info_count.cpp.o +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp -[ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/vitfilter.c -[ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include 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ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-P CMakeFiles/input.dir/cmake_clean_target.cmake -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -cd 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+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 -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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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 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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 +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 72%] Built target hmmer +[ 72%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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] @@ -3398,8 +3433,12 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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()); | ^~~~ -[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:10: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, @@ -3410,149 +3449,85 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/hmm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" +[ 72%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:14: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 72%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/hmm/hmmfile.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' - 251 | ++inner_it_; - | ^~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' - 377 | for (; !it_.IsEnd(); ++it_) { - | ^~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' - 123 | return compressor.Run(); - | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:394:46: required from here - 394 | omnigraph::CompressAllVertices(g_); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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) - | ~~~~~~~^~~ -/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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp -[ 70%] Built target input -[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp -[ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/mpi.c -[ 72%] Linking C static library libhmmer.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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 -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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%] Built target hmmer -[ 72%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp +[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/extract_domains.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:14: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:10: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/extract_domains.cpp +[ 73%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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) + | ~~~~~~~^~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/hmm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 73%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/hmm/hmmfile.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:17, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:12, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:10: @@ -3585,15 +3560,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:9: @@ -3601,16 +3567,11 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp +[ 73%] Linking CXX static library libhmmercpp.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:457:14: warning: unused variable 'u1' [-Wunused-variable] @@ -3623,31 +3584,52 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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; | ^~~~~~~ +/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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 73%] Built target hmmercpp +[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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]': +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp +[ 73%] Linking CXX static library libinput.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp +[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, @@ -3666,8 +3648,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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 projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -3677,67 +3657,32 @@ | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; - | ~~~~^ -[ 73%] Linking CXX static library libhmmercpp.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 73%] Built target hmmercpp -[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp -[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/bits/alloc_traits.h:39, - from /usr/include/c++/15/ext/alloc_traits.h:36, - from /usr/include/c++/15/bits/hashtable_policy.h:39, - from /usr/include/c++/15/bits/hashtable.h:37, - from /usr/include/c++/15/bits/unordered_map.h:33, - from /usr/include/c++/15/unordered_map:43, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node, std::allocator, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 504 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' + 251 | ++inner_it_; + | ^~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' + 377 | for (; !it_.IsEnd(); ++it_) { + | ^~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' + 123 | return compressor.Run(); + | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:394:46: required from here + 394 | omnigraph::CompressAllVertices(g_); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:12: @@ -3745,42 +3690,64 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, - | ^~~~~~~~~~~~~ +/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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 73%] Built target input +[ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, @@ -3804,21 +3771,30 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp:11: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 73%] Linking CXX static library libassembly_graph.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -3846,13 +3822,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:13: @@ -3881,66 +3850,61 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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]': +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 73%] Built target assembly_graph -[ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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()) { - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -3948,12 +3912,73 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/bits/alloc_traits.h:39, + from /usr/include/c++/15/ext/alloc_traits.h:36, + from /usr/include/c++/15/bits/hashtable_policy.h:39, + from /usr/include/c++/15/bits/hashtable.h:37, + from /usr/include/c++/15/bits/unordered_map.h:33, + from /usr/include/c++/15/unordered_map:43, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node, std::allocator, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -3962,6 +3987,13 @@ | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -3976,13 +4008,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -4008,90 +4033,61 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/bits/alloc_traits.h:39, - from /usr/include/c++/15/ext/alloc_traits.h:36, - from /usr/include/c++/15/bits/hashtable_policy.h:39, - from /usr/include/c++/15/bits/hashtable.h:37, - from /usr/include/c++/15/bits/unordered_map.h:33, - from /usr/include/c++/15/unordered_map:43, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: 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=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -/build/reproducible-path/spades-4.0.0+really3.15.5+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]': +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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 74%] Linking CXX static library libassembly_graph.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pe_config_struct.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, from /build/reproducible-path/spades-4.0.0+really3.15.5+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>]', @@ -4129,6 +4125,44 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/bits/alloc_traits.h:39, + from /usr/include/c++/15/ext/alloc_traits.h:36, + from /usr/include/c++/15/bits/hashtable_policy.h:39, + from /usr/include/c++/15/bits/hashtable.h:37, + from /usr/include/c++/15/bits/unordered_map.h:33, + from /usr/include/c++/15/unordered_map:43, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: 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=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: /build/reproducible-path/spades-4.0.0+really3.15.5+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=] @@ -4151,79 +4185,149 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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>]', + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build +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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o +[ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o +[ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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]': +[ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.cpp +[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o +[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o +[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/visualization/position_filler.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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) + | ~~~~~~~~~~~~~~~~^~~~~ +[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp +[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.cpp -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o +[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pacbio/gap_dijkstra.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/visualization/position_filler.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.hpp:14, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pacbio/g_aligner.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_utils.hpp:11, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp:7: @@ -4231,19 +4335,31 @@ 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/alignment/long_read_mapper.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -4259,6 +4375,25 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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(); @@ -4274,23 +4409,16 @@ | ^~~ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -4308,40 +4436,17 @@ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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) - | ~~~~~~~~~~~~~~~~^~~~~ -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/alignment/sequence_mapper_notifier.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp +[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp +[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -4358,12 +4463,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -4371,6 +4470,7 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -4383,19 +4483,62 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, + | ^~~~~~~~~~~~~ +[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -4421,6 +4564,8 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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/overlap_remover.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp 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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: @@ -4431,25 +4576,49 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pipeline/launch_support.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pipeline/launcher.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pipeline/extenders_logic.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/extension_chooser2015.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -4468,117 +4637,21 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-4.0.0+really3.15.5+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>]', - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/bits/alloc_traits.h:39, - from /usr/include/c++/15/ext/alloc_traits.h:36, - from /usr/include/c++/15/bits/hashtable_policy.h:39, - from /usr/include/c++/15/bits/hashtable.h:37, - from /usr/include/c++/15/bits/unordered_map.h:33, - from /usr/include/c++/15/unordered_map:43, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/gap_closer.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>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, - | ^~~~~~~~~~~~~ -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.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> >, 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: 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=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/build/reproducible-path/spades-4.0.0+really3.15.5+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]': +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -4597,65 +4670,17 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.hpp:14, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pacbio/gap_dijkstra.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp -[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, @@ -4684,97 +4709,16 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:402:6: note: declared here 402 | void GenomeConsistenceChecker::Fill() { | ^~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pe_resolver.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/overlap_remover.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pipeline/launch_support.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/pipeline/launcher.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -4804,6 +4748,8 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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, | ^~~~~~~~~~~~~ +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -4813,9 +4759,63 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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/pipeline/extenders_logic.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-4.0.0+really3.15.5+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>]', + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/bits/alloc_traits.h:39, + from /usr/include/c++/15/ext/alloc_traits.h:36, + from /usr/include/c++/15/bits/hashtable_policy.h:39, + from /usr/include/c++/15/bits/hashtable.h:37, + from /usr/include/c++/15/bits/unordered_map.h:33, + from /usr/include/c++/15/unordered_map:43, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/gap_closer.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>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(debruijn_graph::EdgeId) const': +/build/reproducible-path/spades-4.0.0+really3.15.5+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_) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -4835,29 +4835,18 @@ 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: /build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/string:45, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: @@ -4875,21 +4864,6 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 344 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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, - | ^~~~~~~~~~~~~ -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -4918,73 +4892,6 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/scaffold_graph.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(debruijn_graph::EdgeId) const': -/build/reproducible-path/spades-4.0.0+really3.15.5+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_) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -4997,7 +4904,7 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -5016,6 +4923,39 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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], + | ^~~~~~ +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp +[ 81%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -5034,8 +4974,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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/scaffold_graph_constructor.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 @@ -5181,39 +5119,93 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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], - | ^~~~~~ -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:3, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:3, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(debruijn_graph::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -5227,7 +5219,7 @@ from /usr/include/c++/15/string:45, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10: + from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: @@ -5245,6 +5237,86 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -5254,7 +5326,18 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -5268,8 +5351,49 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/string:45, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: 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=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: /build/reproducible-path/spades-4.0.0+really3.15.5+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=] @@ -5292,34 +5416,6 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:3, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:3, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -5327,32 +5423,21 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(debruijn_graph::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 81%] Linking CXX static library libmodules.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -5372,6 +5457,9 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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/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 +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:12: 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>]', @@ -5411,9 +5499,7 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 344 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 +[ 81%] Built target modules 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: /build/reproducible-path/spades-4.0.0+really3.15.5+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=] @@ -5436,66 +5522,16 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/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 -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 81%] Built target modules -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 libspades-stages.a cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 libpath_extend.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 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" /usr/bin/ranlib libspades-stages.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target spades-stages -[ 81%] Linking CXX static library libpath_extend.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 libpath_extend.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -5506,28 +5542,28 @@ make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/config_struct.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/library.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+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/library_data.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp +[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/library_data.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/library.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:8: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp:9: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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() { | ^ @@ -5739,39 +5775,63 @@ make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -[ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o -[ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o -[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.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/subcluster.cpp.o -[ 83%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/construction.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/err_helper_table.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/read_conversion.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/simplification.cpp.o -MF CMakeFiles/stages.dir/simplification.cpp.o.d -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include 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CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/config_struct.cpp -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem 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common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src 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-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-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/genomic_info_filler.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common 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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/err_helper_table.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/construction.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/reference.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp +[ 84%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/genomic_info_filler.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/subcluster.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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_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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_helpers.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/simplification.cpp.o -MF CMakeFiles/stages.dir/simplification.cpp.o.d -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/reference.cpp +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/quality_thresholds_estimator.cpp +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/seqeval/TreephaserLite.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/config_struct.cpp +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/hamcluster_1.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const std::string&, const std::string&, float&, float&, int)': +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:26:56: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] + 26 | if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) + | ~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:28:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] + 28 | num_flows = measurements.size(); + | ~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:46:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] + 46 | unsigned int prefix_size = master_read.sequence.size(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:292:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] + 292 | int backward_idx = seq.size()-1; + | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/reproducible-path/spades-4.0.0+really3.15.5+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); @@ -5799,26 +5859,10 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:514:72: warning: conversion from 'double' to 'float' may change value [-Wfloat-conversion] 514 | child->per_flow_metric = (child->path_metric + 0.5 * penalty1) / child->flow; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const std::string&, const std::string&, float&, float&, int)': -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:26:56: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] - 26 | if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) - | ~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:28:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] - 28 | num_flows = measurements.size(); - | ~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:46:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] - 46 | unsigned int prefix_size = master_read.sequence.size(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:292:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] - 292 | int backward_idx = seq.size()-1; - | ~~~~~~~~~~^~ -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/reference.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/genomic_info_filler.cpp:10: /build/reproducible-path/spades-4.0.0+really3.15.5+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] @@ -5826,33 +5870,28 @@ | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:12: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/construction.cpp:11: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/hamcluster_1.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:12: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/construction.cpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/hkmer.hpp:13, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.hpp:16, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:8: @@ -5869,9 +5908,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/HSeq.hpp:93:36: warning: unused parameter 'size' [-Wunused-parameter] 93 | static size_t GetDataSize(size_t size) { | ~~~~~~~^~~~ -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp -[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/construction.cpp:12: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -5896,19 +5932,10 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp: In static member function 'static bool hammer::correction::TKMerDataEstimator::stage(hammer_config::HammerStage, hammer_config::HammerStage)': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp:90:3: warning: control reaches end of non-void function [-Wreturn-type] 90 | } | ^ -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:12, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:11: @@ -5944,6 +5971,15 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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(); @@ -6005,16 +6041,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:17, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:17: @@ -6063,6 +6089,16 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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 { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ +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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -6407,100 +6443,132 @@ 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/scaffold_correction /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.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[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" +make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake "--color=" +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_converter /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake "--color=" -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 -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gmapper /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake "--color=" -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-4.0.0+really3.15.5+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/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 -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/depend +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/spaligner.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/form_truealignments.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/depend +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build +make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -[ 86%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/positional_read.cpp -[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/main.cpp +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build +make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 87%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build +make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/build +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/build +[ 86%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount/kmer_estimating.cpp -[ 87%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o -[ 87%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -[ 87%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gmapper -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o -MF CMakeFiles/spades-gmapper.dir/main.cpp.o.d -o CMakeFiles/spades-gmapper.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp -make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build +[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o +[ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o +[ 86%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o +make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/positional_read.cpp make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/main.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o +[ 86%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o +[ 86%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o +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 cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount/read_filter.cpp +[ 87%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_converter -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_converter/convert_bin_to_fasta.cpp make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 88%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp -[ 87%] Building CXX object projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_converter -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_converter/convert_bin_to_fasta.cpp -[ 88%] Building CXX object projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount/kmer_estimating.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp [ 88%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/spaligner.dir/align_longreads.cpp.o -MF CMakeFiles/spaligner.dir/align_longreads.cpp.o.d -o CMakeFiles/spaligner.dir/align_longreads.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp +[ 88%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o +[ 89%] Building CXX object projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp -[ 88%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -[ 89%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp -[ 89%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gmapper -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o -MF CMakeFiles/spades-gmapper.dir/main.cpp.o.d -o CMakeFiles/spades-gmapper.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/spaligner.dir/align_longreads.cpp.o -MF CMakeFiles/spaligner.dir/align_longreads.cpp.o.d -o CMakeFiles/spaligner.dir/align_longreads.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp +[ 89%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp +[ 89%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o +[ 89%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp +[ 90%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp +[ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/interesting_pos_processor.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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() { | ^ @@ -6512,8 +6580,8 @@ | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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() { | ^ @@ -6526,8 +6594,30 @@ | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:8: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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() { | ^ @@ -6537,6 +6627,13 @@ 135 | pipeline_type mode = cfg::get().mode; | ^~~~ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:21, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/reproducible-path/spades-4.0.0+really3.15.5+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] @@ -6565,9 +6662,11 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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)); | ^~~~ -[ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o +[ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:24: +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:15: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { @@ -6593,9 +6692,31 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' + 251 | ++inner_it_; + | ^~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' + 377 | for (; !it_.IsEnd(); ++it_) { + | ^~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' + 123 | return compressor.Run(); + | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here + 722 | CompressAllVertices(g_, /*chunk_cnt*/100); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +[ 91%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:15: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { @@ -6621,6 +6742,35 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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], | ^~~~~~ +[ 93%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { @@ -6631,36 +6781,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' - 251 | ++inner_it_; - | ^~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' - 377 | for (; !it_.IsEnd(); ++it_) { - | ^~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' - 123 | return compressor.Run(); - | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here - 722 | CompressAllVertices(g_, /*chunk_cnt*/100); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -6670,6 +6790,16 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -6679,7 +6809,32 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:20: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:21: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { @@ -6690,8 +6845,15 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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], | ^~~~~~ -[ 90%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/main.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)) { @@ -6708,6 +6870,42 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 93%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/main.cpp +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /usr/include/string.h:548, from /usr/include/c++/15/cstring:48, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/mpmc_bounded.hpp:44, @@ -6823,435 +7021,16 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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'; | ^~~~ -[ 90%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp -[ 91%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp -[ 91%] Linking CXX executable ../../bin/spades-truseq-scfcorrection -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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 -[ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/dataset_processor.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-truseq-scfcorrection.dir/link.d "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 -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target spades-truseq-scfcorrection -[ 91%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/__/mts/contig_abundance.cpp.o -MF CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o.d -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/mts/contig_abundance.cpp -[ 91%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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 -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-convert-bin-to-fasta.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 91%] Linking CXX executable ../../bin/spades-kmer-estimating -[ 91%] Built target spades-convert-bin-to-fasta -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 -[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/hamcluster.cpp.o -MF CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-kmer-estimating.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target spades-kmer-estimating -[ 93%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp -[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:12: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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]' - 543 | vm.Start(vals, num_elems, num_threads); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:54:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const std::string&, const KMerData&, dsu::ConcurrentDSU&)::::iterator&, size_t)>]' - 54 | PairSort::InitAndSort(data.data(), blocks.data(), data.size(), data.size() > 1000*16 ? -1 : 1); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:147:21: required from here - 147 | Splitter.split([&] (const std::vector::iterator &start, size_t sz) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 148 | if (sz < block_thr) { - | ~~~~~~~~~~~~~~~~~~~~~ - 149 | // Merge small blocks. - | ~~~~~~~~~~~~~~~~~~~~~~ - 150 | processBlockQuadratic(uf, start, sz, data, tau_); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 151 | } else { - | ~~~~~~~~ - 152 | big_blocks1 += 1; - | ~~~~~~~~~~~~~~~~~ - 153 | // Otherwise - dump for next iteration. - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 154 | for (unsigned i = 0; i < tau_ + 1; ++i) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 155 | serialize(bfs, kfs, - | ~~~~~~~~~~~~~~~~~~~ - 156 | data, &start, sz, - | ~~~~~~~~~~~~~~~~~ - 157 | SubKMerStridedSerializer(i, tau_ + 1)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 158 | } - | ~ - 159 | } - | ~ - 160 | }); - | ~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:42: warning: unused parameter 'num_elems' [-Wunused-parameter] - 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { - | ~~~~~~~^~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:57: warning: unused parameter 'num_threads' [-Wunused-parameter] - 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { - | ~~~~^~~~~~~~~~~ -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': -/build/reproducible-path/spades-4.0.0+really3.15.5+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::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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, - | ^~~~~~~~~~~~~ -[ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/config_struct.cpp -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/form_truealignments.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp -[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/kmer_data.cpp -[ 94%] Linking CXX executable ../../bin/spades-kmercount -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 -[ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/main.cpp -[ 95%] Linking CXX executable ../../bin/spades-read-filter -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 -[ 95%] Linking CXX executable ../../bin/spades-core -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-kmercount.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 95%] Built target spades-kmercount -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 95%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-read-filter.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 95%] Built target spades-read-filter -[ 96%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[ 96%] Linking CXX executable ../../bin/spades-gmapper -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 -[ 96%] Linking CXX executable ../../bin/spaligner -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 -[ 96%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/config_struct_hammer.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 96%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spaligner.dir/link.d 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target spaligner -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-core.dir/link.d "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 -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Linking CXX executable ../../bin/unitig-coverage -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitig-coverage.dir/link.txt --verbose=1 -[ 97%] Built target spades-core -[ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp -[ 97%] Linking CXX executable ../../bin/spades-corrector-core -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-gmapper.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/unitig-coverage.dir/link.d "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 -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target spades-gmapper -[ 97%] Built target unitig-coverage -[ 97%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp -[ 97%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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(); | ^~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-corrector-core.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target spades-corrector-core -[ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/expander.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:20: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:21: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis/CMakeFiles/mag-improve.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Building CXX object projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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], - | ^~~~~~ +[ 93%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp +[ 94%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp +[ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/dataset_processor.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -7318,18 +7097,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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); | ^~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:12: @@ -7387,15 +7154,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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(); @@ -7428,6 +7186,215 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, + | ^~~~~~~~~~~~~ +[ 94%] Linking CXX executable ../../bin/spades-truseq-scfcorrection +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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 +[ 94%] Linking CXX executable ../../bin/spades-kmer-estimating +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-truseq-scfcorrection.dir/link.d "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 +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 94%] Built target spades-truseq-scfcorrection +[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/hamcluster.cpp.o -MF CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-kmer-estimating.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 94%] Built target spades-kmer-estimating +[ 94%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp +[ 94%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-convert-bin-to-fasta.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 94%] Built target spades-convert-bin-to-fasta +[ 95%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:12: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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]' + 543 | vm.Start(vals, num_elems, num_threads); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:54:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const std::string&, const KMerData&, dsu::ConcurrentDSU&)::::iterator&, size_t)>]' + 54 | PairSort::InitAndSort(data.data(), blocks.data(), data.size(), data.size() > 1000*16 ? -1 : 1); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:147:21: required from here + 147 | Splitter.split([&] (const std::vector::iterator &start, size_t sz) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 148 | if (sz < block_thr) { + | ~~~~~~~~~~~~~~~~~~~~~ + 149 | // Merge small blocks. + | ~~~~~~~~~~~~~~~~~~~~~~ + 150 | processBlockQuadratic(uf, start, sz, data, tau_); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 151 | } else { + | ~~~~~~~~ + 152 | big_blocks1 += 1; + | ~~~~~~~~~~~~~~~~~ + 153 | // Otherwise - dump for next iteration. + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 154 | for (unsigned i = 0; i < tau_ + 1; ++i) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 155 | serialize(bfs, kfs, + | ~~~~~~~~~~~~~~~~~~~ + 156 | data, &start, sz, + | ~~~~~~~~~~~~~~~~~ + 157 | SubKMerStridedSerializer(i, tau_ + 1)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 158 | } + | ~ + 159 | } + | ~ + 160 | }); + | ~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:42: warning: unused parameter 'num_elems' [-Wunused-parameter] + 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { + | ~~~~~~~^~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:57: warning: unused parameter 'num_threads' [-Wunused-parameter] + 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { + | ~~~~^~~~~~~~~~~ +[ 95%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/__/mts/contig_abundance.cpp.o -MF CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o.d -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/mts/contig_abundance.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': +/build/reproducible-path/spades-4.0.0+really3.15.5+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::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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: @@ -7456,15 +7423,46 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp +[ 96%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/config_struct.cpp +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis/CMakeFiles/mag-improve.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -7474,6 +7472,84 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 97%] Linking CXX executable ../../bin/spades-read-filter +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +[ 97%] Linking CXX executable ../../bin/spades-kmercount +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 +[ 97%] Linking CXX executable ../../bin/form_truealignments +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-kmercount.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target spades-kmercount +[ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/main.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-read-filter.dir/link.d "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 +[ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/kmer_data.cpp +[ 97%] Built target spades-read-filter +[ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/config_struct_hammer.cpp +[ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/form_truealignments.dir/link.d 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target form_truealignments +[ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/expander.cpp +[ 97%] Linking CXX executable ../../bin/spades-gmapper +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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) { + | ^ +[ 97%] Linking CXX executable ../../bin/spaligner +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; + | ~~~~~~~~~~^~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spaligner.dir/link.d 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target spaligner +[ 97%] Linking CXX executable ../../bin/unitig-coverage +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-gmapper.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target spades-gmapper +[ 97%] Linking CXX executable ../../bin/spades-corrector-core +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/unitig-coverage.dir/link.d "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 +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target unitig-coverage +[ 97%] Linking CXX executable ../../bin/spades-core +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-corrector-core.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target spades-corrector-core In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: @@ -7502,14 +7578,20 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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], | ^~~~~~ -[ 98%] Linking CXX executable ../../bin/spades-hammer -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-core.dir/link.d "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 +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target spades-core +[ 97%] Linking CXX executable ../../bin/cds-mapping-stats +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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 /build/reproducible-path/spades-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -7522,38 +7604,15 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, - | ^~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-hammer.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spades-hammer -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-gbuilder -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-gbuilder.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spades-gbuilder -[ 98%] Linking CXX executable ../../bin/form_truealignments -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/form_truealignments.dir/link.d 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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/cds-mapping-stats.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target form_truealignments +[ 97%] Built target cds-mapping-stats /build/reproducible-path/spades-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -7600,6 +7659,8 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-hammer +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: @@ -7610,16 +7671,19 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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, | ^~~~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-hammer.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target spades-hammer [100%] Linking CXX executable ../../bin/cds-subgraphs cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 +[100%] Linking CXX executable ../../bin/spades-gbuilder +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/cds-subgraphs.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target cds-subgraphs -[100%] Linking CXX executable ../../bin/cds-mapping-stats -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/cds-mapping-stats.dir/link.d "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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-gbuilder.dir/link.d "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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[100%] Built target cds-mapping-stats +[100%] Built target spades-gbuilder /build/reproducible-path/spades-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -7648,44 +7712,16 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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, - | ^~~~~~~~~~~~~ -[100%] Linking CXX executable ../../bin/mag-improve -cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/mag-improve.dir/link.d "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 -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[100%] Built target mag-improve [100%] Linking CXX executable ../../bin/spades-gsimplifier cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gsimplifier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/spades-gsimplifier.dir/link.d "CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o" "CMakeFiles/spades-gsimplifier.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gsimplifier ../../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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target spades-gsimplifier +[100%] Linking CXX executable ../../bin/mag-improve +cd /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -Wl,--dependency-file=CMakeFiles/mag-improve.dir/link.d "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 +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[100%] Built target mag-improve make[3]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 debruijn_test @@ -7696,256 +7732,248 @@ make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' 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[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.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/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.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 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Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/cppformat/CMakeFiles/format.dir/posix.cc.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target gqf Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target gtest +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build +Consolidate compiler generated dependencies of target edlib +Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target format +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". 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Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target version Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/BamDeviceFactory_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". +make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". 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Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/ParallelBgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target coverage_model Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/SamFormatPrinter_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target gqf +Consolidate compiler generated dependencies of target binary_io +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target edlib Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target mimalloc-obj +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target gtest Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target binary_io -make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target coverage_model -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 2%] Built target gqf Consolidate compiler generated dependencies of target paired_info -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 4%] Built target mimalloc-obj make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 -[ 2%] Built target edlib -[ 7%] Built target mimalloc-obj -[ 7%] Built target gqf +[ 7%] Built target edlib [ 9%] Built target format +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 9%] Built target gtest [ 11%] Built target version -[ 11%] Built target gtest make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+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]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 11%] Built target binary_io make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" Consolidate compiler generated dependencies of target BamTools +[ 11%] Built target binary_io +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build +[ 11%] Built target coverage_model Dependencies file "common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target sequence Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". -[ 11%] Built target paired_info -Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target sequence -Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target teamcity_gtest +Consolidate compiler generated dependencies of target llvm-support make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build -[ 11%] Built target coverage_model make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 -Consolidate compiler generated dependencies of target llvm-support +Consolidate compiler generated dependencies of target teamcity_gtest +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build +[ 11%] Built target paired_info make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build -Consolidate compiler generated dependencies of target utils -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build -[ 14%] Built target sequence -[ 14%] Built target teamcity_gtest +Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". +Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 33%] Built target BamTools +[ 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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 33%] Built target sequence make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" -[ 54%] Built target llvm-support -[ 57%] Built target utils +[ 33%] Built target teamcity_gtest Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". @@ -7958,37 +7986,34 @@ Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". 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Dependencies file "ext/samtools/CMakeFiles/samtools.dir/razf.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" +Consolidate compiler generated dependencies of target utils +[ 54%] Built target llvm-support +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build Consolidate compiler generated dependencies of target samtools make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -[ 64%] Built target samtools +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 61%] Built target samtools make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" -Consolidate compiler generated dependencies of target assembly_graph -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 +[ 64%] Built target utils +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" Dependencies file "common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". @@ -7996,40 +8021,51 @@ Dependencies file "common/io/CMakeFiles/input.dir/reads/parser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/sam/read.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target input +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build -[ 69%] Built target assembly_graph +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target assembly_graph +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 +[ 69%] Built target input +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -[ 73%] Built target input -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". +Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/loop_detector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/loop_traverser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/overlap_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/path_extenders.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/pe_config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/pe_resolver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/pipeline/extenders_logic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/pipeline/launch_support.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+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/pipeline/launcher.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". @@ -8045,8 +8081,8 @@ make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target path_extend [ 78%] Built target modules +Consolidate compiler generated dependencies of target path_extend make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -8100,52 +8136,55 @@ make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 92%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_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/simplification_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/io_test.cpp.o -MF CMakeFiles/debruijn_test.dir/io_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/io_test.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/histogram_test.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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_utils.cpp.o -MF CMakeFiles/debruijn_test.dir/test_utils.cpp.o.d -o CMakeFiles/debruijn_test.dir/test_utils.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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_utils.cpp.o -MF CMakeFiles/debruijn_test.dir/test_utils.cpp.o.d -o CMakeFiles/debruijn_test.dir/test_utils.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.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/graph_alignment_test.cpp.o +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/histogram_test.cpp +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/overlap_analysis_test.cpp +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/construction_test.cpp.o -MF CMakeFiles/debruijn_test.dir/construction_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/construction_test.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp +[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/io_test.cpp.o -MF CMakeFiles/debruijn_test.dir/io_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/io_test.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp -[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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_removal_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp -[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/overlap_analysis_test.cpp:8: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:9: +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: /build/reproducible-path/spades-4.0.0+really3.15.5+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() { | ^ @@ -8157,33 +8196,35 @@ | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/overlap_analysis_test.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:9: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp:7: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp:8: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:9: /build/reproducible-path/spades-4.0.0+really3.15.5+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() { | ^ @@ -8223,15 +8264,10 @@ 193 | int read_count = fscanf(file, "%zu\n", &pos_count); | ^~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:8: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp:8: /build/reproducible-path/spades-4.0.0+really3.15.5+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() { | ^ @@ -8245,15 +8281,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -8285,6 +8312,15 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': /build/reproducible-path/spades-4.0.0+really3.15.5+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; @@ -8303,6 +8339,25 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:10: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -8312,40 +8367,9 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:48:62: required from 'debruijn_graph::RandomGraphAccessor::EdgeId debruijn_graph::RandomGraphAccessor::GetRandomEdge() const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' - 48 | for (auto it = graph_.SmartEdgeBegin(); !it.IsEnd(); ++it) { - | ^~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:173:48: required from 'void debruijn_graph::RandomPairedIndex::RemoveRandomEdgeInfo() [with Index = omnigraph::de::PairedIndex]' - 173 | this->value_.Remove(this->GetRandomEdge()); - | ~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:184:13: required from 'void debruijn_graph::RandomPairedIndex::PerformRandomOperation() [with Index = omnigraph::de::PairedIndex]' - 184 | RemoveRandomEdgeInfo(); - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:176:10: required from here - 176 | void PerformRandomOperation() override { - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:40:13: required from 'debruijn_graph::RandomGraphAccessor::VertexId debruijn_graph::RandomGraphAccessor::GetRandomVertex() const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' - 40 | ++it; - | ^~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:100:51: required from 'void debruijn_graph::RandomGraph::AddRandomEdge() [with Graph = debruijn_graph::DeBruijnGraph]' - 100 | this->value_.AddEdge(this->GetRandomVertex(), this->GetRandomVertex(), - | ~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:119:17: required from 'void debruijn_graph::RandomGraph::PerformRandomOperation() [with Graph = debruijn_graph::DeBruijnGraph]' - 119 | AddRandomEdge(); - | ^~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:112:10: required from here - 112 | void PerformRandomOperation() override { - | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:125:55: required from here + 125 | for (auto it = g.SmartEdgeBegin(); !it.IsEnd(); ++it) { + | ^~ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ @@ -8373,25 +8397,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:10: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -8401,9 +8406,40 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:125:55: required from here - 125 | for (auto it = g.SmartEdgeBegin(); !it.IsEnd(); ++it) { - | ^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:48:62: required from 'debruijn_graph::RandomGraphAccessor::EdgeId debruijn_graph::RandomGraphAccessor::GetRandomEdge() const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' + 48 | for (auto it = graph_.SmartEdgeBegin(); !it.IsEnd(); ++it) { + | ^~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:173:48: required from 'void debruijn_graph::RandomPairedIndex::RemoveRandomEdgeInfo() [with Index = omnigraph::de::PairedIndex]' + 173 | this->value_.Remove(this->GetRandomEdge()); + | ~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:184:13: required from 'void debruijn_graph::RandomPairedIndex::PerformRandomOperation() [with Index = omnigraph::de::PairedIndex]' + 184 | RemoveRandomEdgeInfo(); + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:176:10: required from here + 176 | void PerformRandomOperation() override { + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:40:13: required from 'debruijn_graph::RandomGraphAccessor::VertexId debruijn_graph::RandomGraphAccessor::GetRandomVertex() const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' + 40 | ++it; + | ^~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:100:51: required from 'void debruijn_graph::RandomGraph::AddRandomEdge() [with Graph = debruijn_graph::DeBruijnGraph]' + 100 | this->value_.AddEdge(this->GetRandomVertex(), this->GetRandomVertex(), + | ~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:119:17: required from 'void debruijn_graph::RandomGraph::PerformRandomOperation() [with Graph = debruijn_graph::DeBruijnGraph]' + 119 | AddRandomEdge(); + | ^~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:112:10: required from here + 112 | void PerformRandomOperation() override { + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ @@ -8429,44 +8465,62 @@ | ^~~~ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' + 251 | ++inner_it_; + | ^~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' + 377 | for (; !it_.IsEnd(); ++it_) { + | ^~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:275:16: required from here + 275 | remover.Run(); + | ~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -8489,6 +8543,13 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -8498,24 +8559,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' - 251 | ++inner_it_; - | ^~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' - 377 | for (; !it_.IsEnd(); ++it_) { - | ^~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:275:16: required from here - 275 | remover.Run(); - | ~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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]': /build/reproducible-path/spades-4.0.0+really3.15.5+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(); @@ -8549,7 +8592,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -8559,31 +8601,15 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -8612,34 +8638,16 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-4.0.0+really3.15.5+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]': @@ -8706,6 +8714,50 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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]' @@ -8753,14 +8805,14 @@ | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -8806,22 +8858,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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)); | ^~~~~~~~~~ -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -8865,6 +8901,24 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:10: required from here 309 | void HandleDelete(VertexId v) override { @@ -8893,24 +8947,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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); | ^~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; @@ -9057,28 +9093,6 @@ /usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, - 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: -/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ /build/reproducible-path/spades-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -9116,14 +9130,35 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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]': +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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+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 | *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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2152:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:579:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 579 | 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1282:47, + 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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:33: +/usr/include/c++/15/bits/new_allocator.h:151:73: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -9133,6 +9168,10 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -9145,16 +9184,19 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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; | ^~~~~~~~ @@ -9195,12 +9237,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -9479,155 +9515,155 @@ 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+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[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+really3.15.5+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[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-4.0.0+really3.15.5+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[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" +make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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 -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.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-4.0.0+really3.15.5+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 -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. +make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. +make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. +make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 2%] Built target mimalloc-obj make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 4%] Built target format +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 2%] Built target version -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build [ 4%] Built target gtest -[ 4%] Built target mimalloc-obj -[ 9%] Built target gqf -[ 9%] Built target edlib -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend +[ 7%] Built target gqf +[ 7%] 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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" -[ 12%] Built target format -[ 12%] Built target coverage_model -[ 12%] Built target binary_io -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend -[ 12%] Built target paired_info +[ 7%] Built target coverage_model make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 9%] Built target edlib +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" +[ 17%] Built target version [ 31%] Built target BamTools +[ 31%] Built target paired_info make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build -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/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' [ 53%] Built target llvm-support +make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build -[ 56%] Built target teamcity_gtest -[ 56%] Built target sequence make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build +[ 53%] Built target teamcity_gtest make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 56%] Built target sequence make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Built target samtools -[ 65%] Built target utils +[ 63%] Built target samtools make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" +[ 65%] Built target utils +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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 +[ 70%] Built target input make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 70%] Built target input [ 75%] 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 @@ -9680,22 +9716,22 @@ make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' 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-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_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/cyclic_hash_test.cpp.o -[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/sequence_test.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/seq_test.cpp.o -MF CMakeFiles/include_test.dir/seq_test.cpp.o.d -o CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp [ 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/rtseq_test.cpp.o [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o -[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/seq_test.cpp.o -MF CMakeFiles/include_test.dir/seq_test.cpp.o.d -o CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/sequence_test.cpp +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/quality_test.cpp +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/test.cpp +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/binary_test.cpp +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/nucl_test.cpp cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/cyclic_hash_test.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/binary_test.cpp -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/test.cpp In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:7: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 7; T = long unsigned int]', inlined from 'char Seq::first() const [with long unsigned int size_ = 7; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:461:26, @@ -9904,10 +9940,10 @@ make[2]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg' dh_auto_test -O--sourcedirectory=assembler/src -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 + cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j12 +/usr/bin/ctest --force-new-ctest-process --verbose -j16 UpdateCTestConfiguration from :/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu @@ -10073,36 +10109,36 @@ 1: [----------] Global test environment tear-down 1: [==========] 58 tests from 7 test suites ran. (0 ms total) 1: [ PASSED ] 58 tests. -1/2 Test #1: include_test ..................... Passed 0.00 sec +1/2 Test #1: include_test ..................... Passed 0.01 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 / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.Empty (0 ms) +2: 0:00:00.016 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.Empty (37 ms) 2: [ RUN ] GraphCore.OneVertex -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.OneVertex (0 ms) +2: 0:00:00.036 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.052 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.OneVertex (24 ms) 2: [ RUN ] GraphCore.OneEdge -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.OneEdge (0 ms) +2: 0:00:00.060 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.080 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.OneEdge (28 ms) 2: [ RUN ] GraphCore.VertexMethods -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.VertexMethods (0 ms) +2: 0:00:00.088 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.108 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.VertexMethods (28 ms) 2: [ RUN ] GraphCore.SmartIterator -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.SmartIterator (0 ms) +2: 0:00:00.116 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.136 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.SmartIterator (28 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.SelfRCEdgeMerge (0 ms) -2: [----------] 6 tests from GraphCore (1 ms total) +2: 0:00:00.144 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.160 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.SelfRCEdgeMerge (28 ms) +2: [----------] 6 tests from GraphCore (173 ms total) 2: 2: [----------] 1 test from Histogram 2: [ RUN ] Histogram.StrongWeakPtrBasic @@ -10135,10 +10171,10 @@ 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] PairedInfo.RandomSymmetry (27 ms) -2: [----------] 13 tests from PairedInfo (27 ms total) +2: 0:00:00.172 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.180 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] PairedInfo.RandomSymmetry (71 ms) +2: [----------] 13 tests from PairedInfo (71 ms total) 2: 2: [----------] 13 tests from OverlapAnalysis 2: [ RUN ] OverlapAnalysis.Trivial @@ -10177,858 +10213,858 @@ 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: 0:00:00.028 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.028 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.029 1M / 7M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp -2: 0:00:00.029 1M / 7M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started -2: 0:00:00.030 1M / 8M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip -2: [ OK ] Simplification.SimpleTipClipperTest (1 ms) +2: 0:00:00.245 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.248 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.256 1M / 7M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp +2: 0:00:00.264 1M / 7M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started +2: 0:00:00.283 1M / 8M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip +2: [ OK ] Simplification.SimpleTipClipperTest (57 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest -2: 0:00:00.030 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.030 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.030 1M / 8M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:00.030 1M / 8M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.030 1M / 8M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.030 1M / 8M INFO General (graph_simplification.hpp : 645) Creating br instance -2: [ OK ] Simplification.SimpleBulgeRemovalTest (1 ms) +2: 0:00:00.301 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.308 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.316 1M / 8M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:00.324 1M / 8M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.335 1M / 8M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.349 1M / 8M INFO General (graph_simplification.hpp : 645) Creating br instance +2: [ OK ] Simplification.SimpleBulgeRemovalTest (64 ms) 2: [ RUN ] Simplification.TipobulgeTest -2: 0:00:00.031 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.031 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.031 1M / 8M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:00.031 1M / 8M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:00.031 1M / 8M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:00.031 1M / 8M INFO General (graph_simplification.hpp : 645) Creating br instance -2: [ OK ] Simplification.TipobulgeTest (0 ms) +2: 0:00:00.365 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.372 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.380 1M / 8M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:00.388 1M / 8M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:00.398 1M / 8M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.416 1M / 8M INFO General (graph_simplification.hpp : 645) Creating br instance +2: [ OK ] Simplification.TipobulgeTest (68 ms) 2: [ RUN ] Simplification.SimpleECTest -2: 0:00:00.031 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.031 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.031 1M / 8M 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: 0:00:00.031 1M / 8M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.035 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleECTest (10 ms) +2: 0:00:00.432 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.440 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.448 1M / 8M 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: 0:00:00.464 1M / 8M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.484 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleECTest (77 ms) 2: [ RUN ] Simplification.SimpleIterECTest -2: 0:00:00.040 1M / 10M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.040 1M / 10M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.040 1M / 10M 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: 0:00:00.040 1M / 10M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.043 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleIterECTest (8 ms) +2: 0:00:00.515 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.524 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.540 1M / 12M 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: 0:00:00.548 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.559 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleIterECTest (70 ms) 2: [ RUN ] Simplification.IterECTest -2: 0:00:00.048 1M / 10M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.048 1M / 10M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.048 1M / 10M 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: 0:00:00.048 1M / 10M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.051 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.IterECTest (8 ms) +2: 0:00:00.588 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.596 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.604 1M / 12M 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: 0:00:00.612 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.623 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.IterECTest (65 ms) 2: [ RUN ] Simplification.IterUniquePath -2: 0:00:00.057 1M / 10M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.057 1M / 10M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.057 1M / 10M 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: 0:00:00.057 1M / 10M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.059 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: 0:00:00.059 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: 0:00:00.062 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: [ OK ] Simplification.IterUniquePath (10 ms) +2: 0:00:00.654 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.660 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.668 1M / 12M 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: 0:00:00.676 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.687 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: 0:00:00.692 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: 0:00:00.703 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: [ OK ] Simplification.IterUniquePath (65 ms) 2: [ RUN ] Simplification.MFUniquePath -2: 0:00:00.067 1M / 10M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.067 1M / 10M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.067 1M / 10M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp -2: 0:00:00.067 1M / 10M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started -2: 0:00:00.070 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path -2: 0:00:00.070 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy -2: [ OK ] Simplification.MFUniquePath (14 ms) +2: 0:00:00.718 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.724 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.732 1M / 12M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp +2: 0:00:00.744 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started +2: 0:00:00.759 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path +2: 0:00:00.769 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy +2: [ OK ] Simplification.MFUniquePath (77 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge -2: 0:00:00.080 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.080 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.080 1M / 12M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:00.080 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.081 1M / 12M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.081 1M / 12M INFO General (simplification_test.cpp : 276) Done -2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (0 ms) +2: 0:00:00.799 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.808 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.824 1M / 12M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:00.832 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.841 1M / 12M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.864 1M / 12M INFO General (simplification_test.cpp : 276) Done +2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (73 ms) 2: [ RUN ] Simplification.ComplexBulge -2: 0:00:00.081 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.081 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.081 1M / 12M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.081 1M / 12M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:00.081 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:00.085 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:00.085 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:00.095 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.114 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: 0:00:00.114 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.124 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:00.124 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: [ OK ] Simplification.ComplexBulge (54 ms) +2: 0:00:00.873 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.880 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.888 1M / 12M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.896 1M / 12M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:00.904 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.921 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:00.929 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:00.955 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.995 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: 0:00:01.009 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:01.035 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:01.042 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: [ OK ] Simplification.ComplexBulge (207 ms) 2: [ RUN ] Simplification.BigComplexBulge -2: 0:00:00.135 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.135 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.135 1M / 14M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.135 1M / 14M 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: 0:00:00.135 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:00.162 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge -2: 0:00:00.162 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) -2: 0:00:00.170 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.182 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: 0:00:00.182 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.197 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:00.197 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 (74 ms) +2: 0:00:01.084 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.092 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.100 1M / 14M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:01.108 1M / 14M 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: 0:00:01.116 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:01.165 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge +2: 0:00:01.180 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) +2: 0:00:01.207 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.492 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: 0:00:01.500 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:01.528 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:01.537 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 (494 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover -2: 0:00:00.208 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.208 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.208 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.208 1M / 17M 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: 0:00:00.208 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:00.209 1M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:00.209 1M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) -2: 0:00:00.213 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.236 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). -2: 0:00:00.236 2M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.246 2M / 17M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:00.246 2M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:00.246 2M / 17M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover (63 ms) +2: 0:00:01.578 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.584 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.592 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:01.600 1M / 17M 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: 0:00:01.608 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:01.628 1M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:01.637 1M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) +2: 0:00:01.652 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.697 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). +2: 0:00:01.705 2M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:01.736 2M / 17M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:01.745 2M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:01.753 2M / 17M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover (234 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 -2: 0:00:00.272 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.272 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.272 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.272 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:00.272 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:00.275 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:00.275 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:00.284 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.304 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: 0:00:00.304 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.314 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:00.314 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:00.314 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover1 (54 ms) +2: 0:00:01.812 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.824 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.832 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:01.848 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:01.856 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:01.868 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:01.876 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:01.910 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.964 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: 0:00:01.972 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.020 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:02.028 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:02.036 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover1 (260 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 -2: 0:00:00.325 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.325 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.325 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.325 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp -2: 0:00:00.325 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started -2: 0:00:00.326 3M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:00.326 3M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) -2: 0:00:00.326 3M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.327 3M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). -2: 0:00:00.327 3M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.328 3M / 17M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:00.328 3M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:00.328 3M / 17M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover2 (7 ms) +2: 0:00:02.071 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.080 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.088 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.096 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp +2: 0:00:02.104 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started +2: 0:00:02.122 3M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:02.137 3M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) +2: 0:00:02.152 3M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.170 3M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). +2: 0:00:02.176 3M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.200 3M / 17M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:02.208 3M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:02.225 3M / 17M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover2 (184 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 -2: 0:00:00.333 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.333 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.333 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.333 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:00.333 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:00.333 1M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:00.333 1M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) -2: 0:00:00.333 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.334 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). -2: 0:00:00.334 1M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.334 1M / 17M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:00.334 1M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:00.334 1M / 17M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover3 (1 ms) +2: 0:00:02.257 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.264 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.272 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.280 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:02.288 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:02.296 1M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:02.312 1M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) +2: 0:00:02.328 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.345 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). +2: 0:00:02.352 1M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.376 1M / 17M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:02.384 1M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:02.393 1M / 17M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover3 (157 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 -2: 0:00:00.335 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.335 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.335 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.335 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp -2: 0:00:00.335 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started -2: 0:00:00.335 4M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:00.335 4M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) -2: 0:00:00.336 4M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.339 4M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). -2: 0:00:00.339 4M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.341 4M / 17M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:00.341 4M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:00.341 4M / 17M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover4 (15 ms) +2: 0:00:02.416 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.424 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.432 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.440 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp +2: 0:00:02.448 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started +2: 0:00:02.459 4M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:02.469 4M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) +2: 0:00:02.484 4M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.500 4M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). +2: 0:00:02.508 4M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.524 4M / 17M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:02.532 4M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:02.541 4M / 17M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover4 (152 ms) 2: [ RUN ] Simplification.CompressorTest -2: 0:00:00.349 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.349 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.349 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.349 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp -2: 0:00:00.349 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started -2: 0:00:00.350 2M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: 0:00:00.350 2M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) -2: 0:00:00.350 2M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.350 2M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). -2: 0:00:00.350 2M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.350 2M / 17M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:00.350 2M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: [ OK ] Simplification.CompressorTest (1 ms) -2: [----------] 17 tests from Simplification (322 ms total) +2: 0:00:02.568 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.576 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.584 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.592 1M / 17M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp +2: 0:00:02.600 1M / 17M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started +2: 0:00:02.610 2M / 17M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: 0:00:02.626 2M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) +2: 0:00:02.648 2M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.648 2M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). +2: 0:00:02.652 2M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.653 2M / 17M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:02.653 2M / 17M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: [ OK ] Simplification.CompressorTest (85 ms) +2: [----------] 17 tests from Simplification (2411 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread -2: 0:00:00.350 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.350 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.350 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:00.350 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.350 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.350 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.350 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.351 1M / 17M INFO General (kmer_splitters.hpp : 131) Used 2 reads -2: 0:00:00.351 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.352 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:00.352 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:00.352 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.352 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.352 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.352 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.354 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. -2: 0:00:00.354 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.355 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. -2: 0:00:00.356 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.356 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). -2: 0:00:00.356 1M / 17M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:00.392 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:00.393 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:00.393 1M / 17M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:00.393 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:00.393 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:00.393 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:00.393 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:00.393 1M / 17M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:00.393 1M / 17M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:00.393 1M / 17M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:00.393 1M / 17M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:00.393 1M / 17M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:00.393 1M / 17M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread (48 ms) +2: 0:00:02.654 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.654 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.654 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:02.654 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.654 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.655 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.655 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.656 1M / 21M INFO General (kmer_splitters.hpp : 131) Used 2 reads +2: 0:00:02.660 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.662 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:02.662 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.662 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.662 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.662 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.662 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.663 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. +2: 0:00:02.663 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.665 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. +2: 0:00:02.665 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.665 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). +2: 0:00:02.665 1M / 21M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.666 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.666 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.666 1M / 21M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.666 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.666 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:02.666 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.666 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.667 1M / 21M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:02.667 1M / 21M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.667 1M / 21M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.667 1M / 21M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.667 1M / 21M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:02.667 1M / 21M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread (18 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 -2: 0:00:00.399 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.399 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.399 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:00.399 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.399 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.399 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.399 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.400 1M / 17M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:00.400 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.402 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. -2: 0:00:00.402 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:00.402 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.402 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.402 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.402 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.402 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. -2: 0:00:00.402 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.404 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. -2: 0:00:00.404 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.405 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). -2: 0:00:00.405 1M / 17M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:00.443 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:00.443 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:00.443 1M / 17M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:00.443 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:00.443 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:00.443 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:00.443 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:00.443 1M / 17M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:00.443 1M / 17M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:00.443 1M / 17M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:00.443 1M / 17M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:00.443 1M / 17M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:00.443 1M / 17M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread2 (46 ms) +2: 0:00:02.673 1M / 21M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.673 1M / 21M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.673 1M / 21M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:02.673 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.673 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.673 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.673 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.674 1M / 21M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:02.674 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.675 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. +2: 0:00:02.675 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.676 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.676 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.676 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.676 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.677 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. +2: 0:00:02.680 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.682 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. +2: 0:00:02.682 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.683 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). +2: 0:00:02.683 1M / 21M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.683 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.686 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.686 1M / 21M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.686 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.686 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:02.686 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.686 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.686 1M / 21M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:02.686 1M / 21M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.686 1M / 21M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.687 1M / 21M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.687 1M / 21M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:02.687 1M / 21M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread2 (15 ms) 2: [ RUN ] GraphConstruction.SplitThread -2: 0:00:00.445 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.445 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.445 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:00.445 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.445 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.445 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.445 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.446 1M / 17M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:00.446 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.447 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:00.447 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:00.447 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.447 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.447 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.447 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.448 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:00.448 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.449 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:00.449 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.449 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:00.449 1M / 17M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:00.492 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:00.492 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:00.492 1M / 17M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:00.492 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:00.492 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:00.492 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:00.493 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:00.493 1M / 17M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:00.493 1M / 17M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:00.493 1M / 17M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:00.493 1M / 17M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:00.493 1M / 17M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:00.493 1M / 17M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread (52 ms) +2: 0:00:02.688 1M / 21M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.688 1M / 21M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.688 1M / 21M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:02.688 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.689 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.689 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.689 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.690 1M / 21M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:02.692 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.693 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:02.694 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.694 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.694 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.694 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.694 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.695 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:02.695 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.696 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:02.696 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.697 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:02.697 1M / 21M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.697 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.698 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.698 1M / 21M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.698 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.698 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:02.698 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.698 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.698 1M / 21M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:02.698 1M / 21M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.698 1M / 21M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.698 1M / 21M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.698 1M / 21M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:02.699 1M / 21M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread (12 ms) 2: [ RUN ] GraphConstruction.SplitThread2 -2: 0:00:00.497 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.497 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.497 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:00.497 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.497 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.497 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.497 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.498 1M / 17M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:00.498 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.500 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:00.500 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:00.500 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.500 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.500 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.500 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.500 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:00.500 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.502 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:00.502 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.503 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). -2: 0:00:00.503 1M / 17M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:00.543 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:00.543 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:00.544 1M / 17M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:00.544 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:00.544 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted -2: 0:00:00.544 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:00.544 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:00.544 1M / 17M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create -2: 0:00:00.544 1M / 17M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:00.544 1M / 17M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:00.544 1M / 17M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:00.544 1M / 17M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:00.544 1M / 17M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread2 (50 ms) +2: 0:00:02.701 1M / 21M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.701 1M / 21M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.701 1M / 21M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:02.701 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.701 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.701 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.704 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.705 1M / 21M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:02.705 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.706 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:02.706 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.706 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.707 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.707 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.707 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.708 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:02.712 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.714 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:02.714 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.714 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). +2: 0:00:02.714 1M / 21M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.715 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.715 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.717 1M / 21M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.717 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.717 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted +2: 0:00:02.717 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.717 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.717 1M / 21M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create +2: 0:00:02.717 1M / 21M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.717 1M / 21M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.717 1M / 21M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.717 1M / 21M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:02.717 1M / 21M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread2 (17 ms) 2: [ RUN ] GraphConstruction.Buldge -2: 0:00:00.547 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.547 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.547 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:00.547 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.547 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.547 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.547 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.548 1M / 17M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:00.548 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.549 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:00.550 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:00.550 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.550 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.550 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.550 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.550 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. -2: 0:00:00.550 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.552 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:00.552 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.553 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:00.553 1M / 17M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:00.595 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:00.595 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:00.595 1M / 17M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:00.595 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:00.595 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted -2: 0:00:00.595 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:00.595 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:00.595 1M / 17M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create -2: 0:00:00.595 1M / 17M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:00.595 1M / 17M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:00.596 1M / 17M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:00.596 1M / 17M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:00.596 1M / 17M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.Buldge (54 ms) +2: 0:00:02.720 1M / 21M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.720 1M / 21M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.720 1M / 21M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:02.720 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.721 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.721 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.721 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.721 1M / 21M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:02.722 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.723 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:02.728 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.728 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.728 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.728 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.728 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.729 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. +2: 0:00:02.729 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.731 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:02.731 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.731 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:02.731 1M / 21M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.732 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.736 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.737 1M / 21M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.737 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.737 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted +2: 0:00:02.737 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.737 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.737 1M / 21M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create +2: 0:00:02.737 1M / 21M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.737 1M / 21M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.737 1M / 21M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.737 1M / 21M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:02.737 1M / 21M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.Buldge (17 ms) 2: [ RUN ] GraphConstruction.CondenseSimple -2: 0:00:00.601 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.601 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.601 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:00.601 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.601 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.601 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.601 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.602 1M / 17M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:00.602 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.603 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:00.604 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:00.604 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.604 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.604 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.604 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.604 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:00.604 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.606 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:00.606 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.606 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:00.606 1M / 17M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:00.644 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:00.644 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:00.644 1M / 17M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:00.644 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:00.644 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:00.644 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:00.644 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:00.645 1M / 17M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:00.645 1M / 17M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:00.645 1M / 17M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:00.645 1M / 17M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:00.645 1M / 17M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:00.645 1M / 17M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.CondenseSimple (48 ms) +2: 0:00:02.737 1M / 21M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.737 1M / 21M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.737 1M / 21M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:02.737 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.737 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.737 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.737 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.738 1M / 21M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:02.738 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.739 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:02.744 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.744 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.744 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.744 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.744 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.745 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:02.745 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.747 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:02.747 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.747 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:02.747 1M / 21M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.748 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.749 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.752 1M / 21M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.752 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.752 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:02.753 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.753 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.753 1M / 21M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:02.753 1M / 21M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.753 1M / 21M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.753 1M / 21M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.753 1M / 21M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:02.753 1M / 21M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.CondenseSimple (16 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex -2: 0:00:00.648 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.648 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.648 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.648 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:00.648 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.649 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.649 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.649 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.649 1M / 17M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:00.650 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.651 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:00.651 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:00.651 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.651 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.651 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.651 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.651 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:00.651 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.653 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:00.653 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.653 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:00.653 1M / 17M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:00.694 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:00.695 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:00.695 1M / 17M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:00.695 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:00.695 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:00.695 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:00.695 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:00.695 1M / 17M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:00.695 1M / 17M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:00.695 1M / 17M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:00.695 1M / 17M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:00.695 1M / 17M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:00.695 1M / 17M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:00.701 1M / 17M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:00.701 1M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:00.701 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.701 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:00.701 1M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerStoringIndex (53 ms) +2: 0:00:02.754 1M / 21M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.754 1M / 21M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.754 1M / 21M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.754 1M / 21M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:02.754 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.754 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.754 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.754 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.755 1M / 21M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:02.755 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.756 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:02.759 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.759 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.759 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.759 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.759 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.760 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:02.760 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.762 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:02.764 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.765 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:02.765 1M / 21M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.766 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.768 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.769 1M / 21M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.769 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.769 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:02.769 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.769 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.769 1M / 21M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:02.769 1M / 21M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.769 1M / 21M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.769 1M / 21M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.769 1M / 21M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:02.769 1M / 21M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:02.769 1M / 21M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:02.770 1M / 21M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:02.770 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.770 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:02.770 1M / 21M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerStoringIndex (17 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex -2: 0:00:00.701 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.701 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.701 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.701 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:00.701 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.701 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.701 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.701 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.702 1M / 17M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:00.702 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.703 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:00.703 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:00.703 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.703 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.703 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.703 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.704 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:00.704 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.705 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:00.705 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.706 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:00.706 1M / 17M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:00.745 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:00.745 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:00.745 1M / 17M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:00.745 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:00.745 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:00.745 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:00.745 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:00.745 1M / 17M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:00.745 1M / 17M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:00.745 1M / 17M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:00.745 1M / 17M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:00.745 1M / 17M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:00.745 1M / 17M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:00.746 1M / 17M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:00.746 1M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:00.746 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.746 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:00.746 1M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerFreeIndex (45 ms) +2: 0:00:02.770 1M / 21M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.776 1M / 21M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.776 1M / 21M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.776 1M / 21M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:02.776 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.776 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.776 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.776 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.777 1M / 21M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:02.777 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.779 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:02.779 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.779 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.779 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.779 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.779 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.780 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:02.780 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.781 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:02.785 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.786 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:02.792 1M / 21M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.793 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.793 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.793 1M / 21M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.793 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.793 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:02.794 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.794 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.794 1M / 21M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:02.794 1M / 21M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.794 1M / 21M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.794 1M / 21M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.794 1M / 21M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:02.794 1M / 21M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:02.795 1M / 21M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:02.795 1M / 21M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:02.795 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.795 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:02.795 1M / 21M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerFreeIndex (25 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo -2: 0:00:00.747 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.747 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.747 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.747 1M / 17M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 -2: 0:00:00.747 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.747 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.747 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.747 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.748 1M / 17M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:00.748 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.749 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. -2: 0:00:00.749 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:00.749 1M / 17M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:00.749 1M / 17M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:00.749 1M / 17M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:00.749 1M / 17M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:00.749 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. -2: 0:00:00.749 1M / 17M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:00.750 1M / 17M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:00.750 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.751 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). -2: 0:00:00.751 1M / 17M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:00.794 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:00.795 1M / 17M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:00.795 1M / 17M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:00.795 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:00.795 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted -2: 0:00:00.795 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:00.795 1M / 17M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:00.795 1M / 17M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create -2: 0:00:00.795 1M / 17M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:00.795 1M / 17M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:00.795 1M / 17M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:00.795 1M / 17M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create -2: 0:00:00.795 1M / 17M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:00.798 1M / 17M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:00.798 1M / 17M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) -2: 0:00:00.798 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.798 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). -2: 0:00:00.798 1M / 17M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.798 1M / 17M INFO General (graph_construction.hpp : 93) Filling coverage index -2: 0:00:00.798 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.799 1M / 17M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). -2: 0:00:00.799 1M / 17M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. -2: 0:00:00.799 1M / 17M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM -2: 0:00:00.799 1M / 17M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process -2: 0:00:00.799 1M / 17M INFO General (graph_pack.cpp : 79) Normalizing done -2: 0:00:00.802 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed -2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (58 ms) -2: [----------] 9 tests from GraphConstruction (454 ms total) +2: 0:00:02.796 1M / 21M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.796 1M / 21M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.796 1M / 21M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.796 1M / 21M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 +2: 0:00:02.796 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.796 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.796 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.796 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.797 1M / 21M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:02.797 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.799 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. +2: 0:00:02.799 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.799 1M / 21M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.799 1M / 21M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.799 1M / 21M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.799 1M / 21M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.800 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. +2: 0:00:02.800 1M / 21M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.802 1M / 21M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:02.802 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.802 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). +2: 0:00:02.802 1M / 21M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.803 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.803 1M / 21M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.803 1M / 21M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.804 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.804 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted +2: 0:00:02.804 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.804 1M / 21M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.804 1M / 21M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create +2: 0:00:02.804 1M / 21M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.804 1M / 21M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.804 1M / 21M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.805 1M / 21M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create +2: 0:00:02.805 1M / 21M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:02.805 1M / 21M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:02.805 1M / 21M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) +2: 0:00:02.805 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.805 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). +2: 0:00:02.805 1M / 21M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.805 1M / 21M INFO General (graph_construction.hpp : 93) Filling coverage index +2: 0:00:02.805 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.806 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). +2: 0:00:02.806 1M / 21M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. +2: 0:00:02.806 1M / 21M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM +2: 0:00:02.806 1M / 21M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process +2: 0:00:02.806 1M / 21M INFO General (graph_pack.cpp : 79) Normalizing done +2: 0:00:02.811 10M / 24M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed +2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (18 ms) +2: [----------] 9 tests from GraphConstruction (159 ms total) 2: 2: [----------] 3 tests from Io 2: [ RUN ] Io.Order -2: 0:00:00.804 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.804 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.829 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.829 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] Io.Order (25 ms) +2: 0:00:02.814 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.814 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.842 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.843 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] Io.Order (30 ms) 2: [ RUN ] Io.PairedInfo 2: [ OK ] Io.PairedInfo (2 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (1 ms) -2: [----------] 3 tests from Io (28 ms total) +2: [----------] 3 tests from Io (33 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor -2: 0:00:00.832 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.832 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.832 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.832 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.832 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathConstructor (0 ms) +2: 0:00:02.846 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.847 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.847 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.847 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.849 1M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathConstructor (4 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove -2: 0:00:00.832 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.832 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.832 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.832 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:02.850 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.850 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.850 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.850 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.851 1M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemove (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps -2: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:02.851 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.851 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.851 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.851 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.851 1M / 24M 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: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:02.852 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.852 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.852 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.852 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.852 1M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathEquals (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathSubpaths -2: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathSubpaths (0 ms) +2: 0:00:02.852 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.852 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.853 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.853 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.853 1M / 24M 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: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:02.853 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.853 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.853 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.853 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.854 1M / 24M 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: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.833 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.833 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:02.854 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.854 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.854 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.854 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.854 1M / 24M 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: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.834 1M / 20M 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 (1 ms total) +2: 0:00:02.855 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.855 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.855 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.855 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.855 1M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathLoopDetector (1 ms) +2: [----------] 8 tests from PathExtend (9 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff -2: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:02.855 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.855 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.855 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.855 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.856 1M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] OverlapRemoval.BasicNoDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicDiff -2: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:02.856 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.856 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.856 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.856 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.856 1M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] OverlapRemoval.BasicDiff (1 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatConjugateEdges -2: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: 0:00:00.834 1M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) +2: 0:00:02.856 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.857 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.857 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:02.857 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:02.857 1M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:02.857 1M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (1 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat -2: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.834 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.834 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.838 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.838 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeat (4 ms) +2: 0:00:02.857 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.857 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.857 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.857 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.868 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.869 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeat (11 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven -2: 0:00:00.838 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.838 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.838 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.838 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.842 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.842 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatUneven (4 ms) +2: 0:00:02.869 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.869 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.869 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.869 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.875 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.875 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatUneven (6 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected -2: 0:00:00.842 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.842 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.842 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.842 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.846 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.846 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.846 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (4 ms) +2: 0:00:02.876 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.876 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.876 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.876 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.882 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.882 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.882 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect -2: 0:00:00.846 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.847 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.847 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.847 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.850 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.850 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (4 ms) +2: 0:00:02.883 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.883 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.883 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.883 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.889 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.889 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd -2: 0:00:00.850 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.850 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.850 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.850 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.854 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.854 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.854 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEnd (4 ms) +2: 0:00:02.889 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.890 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.890 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.890 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.896 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.896 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.896 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEnd (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain -2: 0:00:00.854 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.854 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.854 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.854 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.858 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.858 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.858 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (3 ms) +2: 0:00:02.897 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.897 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.897 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.897 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.903 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.903 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.903 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart -2: 0:00:00.858 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.858 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.858 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.858 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.862 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.862 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.862 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStart (4 ms) +2: 0:00:02.904 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.904 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.904 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.904 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.910 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.910 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.910 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStart (6 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain -2: 0:00:00.862 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.862 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.862 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.862 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.866 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.866 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.867 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (5 ms) +2: 0:00:02.911 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.911 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.911 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.911 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.917 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.917 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.917 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (6 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication -2: 0:00:00.867 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.867 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.867 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.867 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.870 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplication (4 ms) +2: 0:00:02.918 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.918 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.918 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.918 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.924 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplication (6 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual -2: 0:00:00.870 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.870 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.870 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.870 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.874 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (3 ms) +2: 0:00:02.925 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.925 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.925 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.925 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.931 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (7 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff -2: 0:00:00.874 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.874 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.874 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.874 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.878 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiff (4 ms) +2: 0:00:02.931 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.932 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.932 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.932 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.937 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiff (6 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap -2: 0:00:00.878 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.878 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.878 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.878 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.882 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiffGap (5 ms) +2: 0:00:02.938 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.938 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.938 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.938 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.944 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiffGap (7 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 -2: 0:00:00.882 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.882 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.882 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.882 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.887 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (4 ms) +2: 0:00:02.944 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.944 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.945 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.945 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.950 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (6 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 -2: 0:00:00.887 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.887 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.887 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.887 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.891 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (4 ms) +2: 0:00:02.951 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.951 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.951 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.951 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.957 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (6 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen -2: 0:00:00.891 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.891 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.891 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.891 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.895 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.895 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.895 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (4 ms) +2: 0:00:02.957 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.957 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.958 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.958 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.963 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.964 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.964 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (7 ms) 2: [ RUN ] OverlapRemoval.Tricky0 -2: 0:00:00.895 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.895 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.895 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.895 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.898 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.898 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.898 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky0 (4 ms) +2: 0:00:02.964 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.965 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.965 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.965 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.970 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.970 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.971 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky0 (7 ms) 2: [ RUN ] OverlapRemoval.Tricky1 -2: 0:00:00.898 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.898 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.898 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.898 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.902 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.902 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.902 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky1 (4 ms) +2: 0:00:02.971 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.971 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.971 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.972 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.977 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.977 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.977 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky1 (6 ms) 2: [ RUN ] OverlapRemoval.Tricky2 -2: 0:00:00.902 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.902 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.902 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.902 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.906 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.906 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.906 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky2 (3 ms) +2: 0:00:02.978 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.978 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.978 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.979 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.984 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.984 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.984 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky2 (6 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen -2: 0:00:00.906 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.906 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.906 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.906 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.910 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.911 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.911 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicMinEdgeLen (5 ms) +2: 0:00:02.985 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.985 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.985 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.985 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.991 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.991 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.991 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicMinEdgeLen (7 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle -2: 0:00:00.911 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.911 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.911 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.911 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.915 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.915 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:00.915 4M / 20M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.OverlapWithMiddle (4 ms) -2: [----------] 23 tests from OverlapRemoval (81 ms total) +2: 0:00:02.992 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.992 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.992 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.992 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.998 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:02.998 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:02.998 4M / 24M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.OverlapWithMiddle (7 ms) +2: [----------] 23 tests from OverlapRemoval (143 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest -2: 0:00:00.915 1M / 20M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 -2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) +2: 0:00:02.999 1M / 24M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 +2: [ OK ] GraphAligner.EdlibSHWFULLTest (1 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero -2: 0:00:00.915 1M / 20M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 -2: 0:00:00.915 1M / 20M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 -2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (1 ms) +2: 0:00:02.999 1M / 24M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 +2: 0:00:02.999 1M / 24M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 +2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest -2: 0:00:00.915 1M / 20M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.915 1M / 20M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.915 1M / 20M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:00.915 1M / 20M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:00.919 4M / 20M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:00.924 5M / 22M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm -2: [ OK ] GraphAligner.TrivialTest (311 ms) +2: 0:00:02.999 1M / 24M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.999 1M / 24M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.999 1M / 24M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.999 1M / 24M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:03.005 4M / 24M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:03.014 5M / 25M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm +2: [ OK ] GraphAligner.TrivialTest (352 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest -2: 0:00:01.227 1M / 28M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.227 1M / 28M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.227 1M / 28M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:01.227 1M / 28M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:01.230 4M / 28M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraOneEdgeTest (4 ms) +2: 0:00:03.352 1M / 31M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:03.352 1M / 31M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:03.352 1M / 31M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:03.352 1M / 31M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:03.356 4M / 31M 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: 0:00:01.231 1M / 28M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.231 1M / 28M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.231 1M / 28M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:01.231 1M / 28M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:01.234 4M / 28M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:03.356 1M / 31M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:03.356 1M / 31M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:03.356 1M / 31M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:03.356 1M / 31M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:03.360 4M / 31M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraGrowEndsTest (4 ms) -2: [----------] 5 tests from GraphAligner (320 ms total) +2: [----------] 5 tests from GraphAligner (362 ms total) 2: 2: [----------] Global test environment tear-down -2: [==========] 98 tests from 10 test suites ran. (1235 ms total) +2: [==========] 98 tests from 10 test suites ran. (3361 ms total) 2: [ PASSED ] 98 tests. -2/2 Test #2: debruijn_test .................... Passed 1.24 sec +2/2 Test #2: debruijn_test .................... Passed 3.37 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 1.26 sec +Total Test time (real) = 3.39 sec make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+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 -j12 install DESTDIR=/build/reproducible-path/spades-4.0.0\+really3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/reproducible-path/spades-4.0.0\+really3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -11050,28 +11086,28 @@ -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/bin/spades_init.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/VERSION -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.gff --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.txt -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.txt -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.gff --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.txt +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.gff -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R1.fastq.gz --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R1.fastq.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R2.fastq.gz +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R1.fastq.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R2.fastq.gz +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R1.fastq.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KS.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms/Phan-CoV.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz @@ -11083,27 +11119,27 @@ -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/GPLv2.txt -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/bin/spades-core -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/pe_params.info -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/tsa.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/toy.info -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/moleculo_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/pe_params.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/config.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/simplification.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/moleculo_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/construction.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/simplification.info -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/bin/spades-hammer -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/hammer -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/configs/hammer/config.info @@ -11133,50 +11169,50 @@ -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/options_storage.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/options_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/copy_files.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/postprocessing_script.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/plasmid_glue.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_contigs.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_interlaced_reads.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/plasmid_glue.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/correction_iteration_script.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/breaking_scaffolds_script.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/check_test_script.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/postprocessing_script.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/copy_files.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/compress_all.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_contigs.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/breaking_scaffolds_script.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/postprocessing_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/pipeline.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/error_correction_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/check_test_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/preprocess_reads_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/stage.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/correction_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/__init__.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/breaking_scaffolds_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/preprocess_reads_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/terminating_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_iteration_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/breaking_scaffolds_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/__init__.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/before_start_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/postprocessing_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_iteration_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/launch_options.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_filter_contigs.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/barcode_extraction.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_postprocessing.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/string_dist_utils.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/generate_quality.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/id_generation.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/string_dist_utils.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_filter_contigs.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/launch_options.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/reference_construction.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/__init__.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_postprocessing.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/break_by_coverage.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/reference_construction.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/barcode_extraction.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/SeqIO.py --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/sam_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/alignment.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/SeqIO.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/__init__.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/parallel_launcher.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/sam_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors --- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_local.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_save_yaml.py -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executors.py +-- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_local.py make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg' @@ -11234,12 +11270,14 @@ 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/741642/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/741642/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/418759 and its subdirectories -I: Current time: Wed Oct 22 17:19:58 -12 2025 -I: pbuilder-time-stamp: 1761196798 +I: removing directory /srv/workspace/pbuilder/741642 and its subdirectories +I: Current time: Thu Nov 26 01:55:51 +14 2026 +I: pbuilder-time-stamp: 1795607751