Diff of the two buildlogs: -- --- b1/build.log 2025-07-22 09:03:06.206998120 +0000 +++ b2/build.log 2025-07-22 09:14:11.863775855 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 24 02:54:04 -12 2026 -I: pbuilder-time-stamp: 1787583244 +I: Current time: Tue Jul 22 23:03:09 +14 2025 +I: pbuilder-time-stamp: 1753174989 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -43,52 +43,84 @@ dpkg-source: info: applying raw_regex_pattern.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1829647/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2385081/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Jul 22 09:03 /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/2385081/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2385081/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=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fe4dad7e80a4420496945bc831fdcd4b' - 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='1829647' - PS1='# ' - PS2='> ' + INVOCATION_ID=a7a932a22fdc4957a75e40fb1e77b19d + 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=2385081 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.vsv1DX5O/pbuilderrc_sBT6 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vsv1DX5O/b1 --logfile b1/build.log spades_4.0.0+really3.15.5+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.vsv1DX5O/pbuilderrc_iMTL --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vsv1DX5O/b2 --logfile b2/build.log spades_4.0.0+really3.15.5+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1829647/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2385081/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -358,7 +390,7 @@ Get: 186 http://deb.debian.org/debian trixie/main amd64 lynx amd64 2.9.2-1 [641 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.5-1 [1048 B] Get: 188 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.4.2-4 [216 kB] -Fetched 201 MB in 7s (28.9 MB/s) +Fetched 201 MB in 22s (8982 kB/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 ... 19850 files and directories currently installed.) @@ -968,8 +1000,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Aug 24 14:55:56 UTC 2026. -Universal Time is now: Mon Aug 24 14:55:56 UTC 2026. +Local time is now: Tue Jul 22 09:05:37 UTC 2025. +Universal Time is now: Tue Jul 22 09:05:37 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -1145,7 +1177,11 @@ 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-1_source.changes +I: user script /srv/workspace/pbuilder/2385081/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2385081/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-1_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 4.0.0+really3.15.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1419,8 +1455,8 @@ to work with policies introduced by or earlier. --- Configuring done (74.6s) --- Generating done (1.6s) +-- Configuring done (16.0s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -1434,7 +1470,7 @@ 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 -j42 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j40 "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 @@ -1445,186 +1481,179 @@ make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-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/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 -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.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=" +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/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=" -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/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/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/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/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 common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-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[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[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 ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.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/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[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=" +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 -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make -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/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=" +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 -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/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=" +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[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]: 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/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=" +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/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]: 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[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/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[4]: 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[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 -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/build +make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.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 -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' -[ 1%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o -[ 1%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -[ 1%] 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/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 -[ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.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 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6%] 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 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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 -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 +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/common/utils /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu 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/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 -[ 8%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o +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 -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/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build -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]: 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' 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[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 8%] 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/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 -[ 8%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o -[ 8%] 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 -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 -[ 8%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o +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/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/build -[ 8%] 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/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 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/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 -make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build +[ 0%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o +[ 0%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o +[ 0%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o +[ 0%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o +[ 0%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o +[ 0%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o +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/gfa1/CMakeFiles/gfa1.dir/gfa.c.o +[ 1%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o +[ 1%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o +make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/build +[ 1%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o +[ 1%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o +[ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o +[ 1%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o +[ 1%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o +[ 1%] 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/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 +[ 2%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o +[ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o +[ 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/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/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o +[ 3%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o +[ 3%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o +[ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o +[ 3%] 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/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 +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 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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/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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-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 +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 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp -[ 8%] Building C object ext/easel/CMakeFiles/easel.dir/easel.c.o -[ 8%] 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/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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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 -[ 9%] Linking CXX static library libversion.a +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 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp +[ 6%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o +[ 6%] 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 +[ 6%] 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/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 +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 +[ 8%] 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 -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/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); @@ -1633,6 +1662,7 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %02lx +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/ext/src/gqf/gqf.c: In function 'qf_dump': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:641:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 641 | printf("%llu %llu %llu\n", @@ -1666,6 +1696,8 @@ | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} +[ 8%] 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 /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); @@ -1673,8 +1705,16 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 9%] 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 +[ 9%] 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 +/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' +[ 9%] Built target version +[ 9%] 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 +[ 9%] 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 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] @@ -1795,6 +1835,8 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:196:53: note: in expansion of macro 'MI_FORWARD2' 196 | void* __libc_realloc(void* p, size_t size) MI_FORWARD2(mi_realloc,p,size); | ^~~~~~~~~~~ +[ 9%] 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 In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:38: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c: In function 'bool _mi_heap_init()': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c:192:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'mi_heap_t' {aka 'struct mi_heap_s'} with no trivial copy-assignment [-Wclass-memaccess] @@ -1803,108 +1845,74 @@ /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 { | ^~~~~~~~~ +[ 9%] 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 +[ 9%] 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 [ 10%] 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 -/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' -[ 10%] Built target version -[ 10%] 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 -[ 10%] 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 -[ 10%] 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 -[ 10%] Linking C static library libgqf.a +[ 10%] 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 +[ 11%] 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 +[ 11%] 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 +[ 12%] 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 +[ 12%] 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 +[ 12%] 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 +[ 12%] 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 +[ 12%] 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 +[ 12%] 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 +[ 12%] 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 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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/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 +[ 13%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o +[ 13%] Linking C static library libgqf.a +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 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 -[ 10%] 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 -[ 11%] 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 -[ 11%] 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 -[ 11%] 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 -/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' -[ 11%] Built target gfa1 -[ 11%] 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 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 -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=" -[ 11%] 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 +[ 13%] 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 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/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 -[ 11%] 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 -[ 11%] 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 -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; - | ^~~~~~~~ +[ 13%] 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 +[ 13%] 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 +[ 13%] Built target gqf +[ 13%] 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 +[ 15%] 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 +[ 15%] 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 +[ 15%] 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 +[ 15%] 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 +[ 15%] 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 +[ 15%] 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 +[ 15%] 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 +[ 15%] 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 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/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 '< >' -[ 11%] 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 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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/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 -[ 13%] 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 -[ 13%] 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 -[ 15%] 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 -[ 15%] 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 -[ 16%] 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 -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.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/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 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, @@ -1914,101 +1922,195 @@ 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/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 -[ 16%] 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 -[ 17%] 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 -[ 17%] 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 -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o +[ 15%] 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 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+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/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp +[ 15%] 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 +[ 16%] 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 +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 +[ 17%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o +[ 17%] 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/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 +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 +/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' +[ 17%] 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 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp +[ 17%] Built target getopt_pp +[ 18%] 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 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-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 +[ 18%] 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 +[ 18%] 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 +[ 18%] 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 -[ 17%] 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 -[ 17%] 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/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 -[ 17%] 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 -[ 17%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.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/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/WithColor.cpp -[ 17%] 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 -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 '< >' -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 '< >' +[ 18%] 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 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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 +[ 19%] 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 +[ 19%] 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 +[ 19%] 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 +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] + 73 | #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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); + | ^~~~~~~~~~ +[ 19%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o +cd 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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/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 +[ 19%] 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 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: + 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 '< >' -[ 17%] 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 -[ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -[ 18%] 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/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 -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 -[ 18%] 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 -[ 18%] 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 -[ 18%] 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 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 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/YAMLParser.cpp -[ 19%] 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 -[ 20%] 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 -/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++; - | ^ -[ 20%] 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 -[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.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/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 -[ 20%] 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 +[ 19%] 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 +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] + 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) + | ^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:236:9: note: in expansion of macro 'netwrite' + 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); + | ^~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': +/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] + 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) + | ^~~~~~~~~~~~~~~~~~~ +/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); + | ^~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~ +/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/bamtools/api/internal/io/pbgzf/block.c:4: +/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); + | ^~~~~~~~~~~ +/usr/bin/ar qc libgfa1.a CMakeFiles/gfa1.dir/gfa.c.o +/usr/bin/ranlib libgfa1.a +[ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.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/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 +[ 20%] Built target gfa1 +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' +[ 20%] 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 +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); + | ^~~~~~~~~~~~~~~~~ +/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/bamtools/api/internal/io/pbgzf/consumer.c:11: +/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); + | ^~~~~~~~~~~ +[ 22%] 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 +/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_ ? + | ^~~~~~~ +[ 22%] 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 +[ 22%] 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 +[ 22%] 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 +[ 22%] 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 /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); | ^~~~~~ -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/smoothing_distance_estimation.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/smoothing_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 '< >' -[ 20%] 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 +[ 22%] 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 +/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", + | ~~~^ + | | + | long long int + | %ld + 345 | q->mem, q->head, q->tail, q->n, q->length, q->id, q->ordered, q->num_adders, q->num_getters); + | ~~~~~ + | | + | int64_t {aka long int} +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h: At top level: +/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); + | ^~~~~~~~~~~~~~~~~ +/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/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); + | ^~~~~~~~~~~~~~~~~ +/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/bamtools/api/internal/io/pbgzf/pbgzf.c:13: +/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); + | ^~~~~~~~~~~ +/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' +[ 22%] Built target edlib +[ 22%] 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 +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); + | ^~~~~~~~~~~~~~~~~ +/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/bamtools/api/internal/io/pbgzf/reader.c:7: +/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); + | ^~~~~~~~~~~ +[ 23%] 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 +[ 24%] 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 +[ 24%] 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 /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); @@ -2079,19 +2181,151 @@ /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); | ^~~~~~ -[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.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/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 +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 + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/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/bamtools/api/internal/io/pbgzf/writer.c:7: +/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); + | ^~~~~~~~~~~ +[ 24%] 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 +[ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o +[ 24%] 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 +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 +[ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_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/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 +[ 24%] 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 +[ 24%] 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 +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; + | ^~~~~~~~ +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 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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 +[ 25%] 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 +[ 25%] 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 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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/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 +[ 26%] 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 +[ 26%] 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 +[ 26%] 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 +[ 26%] 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 +[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.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/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/WithColor.cpp +[ 26%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o +[ 26%] 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/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 +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 +[ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o +[ 27%] 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 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-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/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/YAMLParser.cpp +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/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 +[ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.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/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/llvm/raw_os_ostream.cpp -[ 20%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o +/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], + | ^~~~~~ +[ 27%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o +[ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.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/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 +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 +[ 27%] 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 +[ 27%] 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 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: + 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 '< >' +[ 29%] 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 +[ 29%] 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 +[ 29%] 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 +[ 30%] 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 +[ 30%] 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 +[ 31%] 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 +[ 31%] 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 +/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++; + | ^ +[ 31%] 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 +/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' +[ 31%] 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 +[ 31%] Built target format +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 31%] 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 +[ 31%] Built target mimalloc-obj +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' +[ 31%] 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 +[ 31%] 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 +[ 32%] 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]' @@ -2103,303 +2337,143 @@ /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); | ^~~ -[ 20%] 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 -[ 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 -[ 20%] 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 -[ 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 -[ 22%] 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 -[ 23%] 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 -/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 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' -[ 23%] Built target getopt_pp -[ 23%] 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 -[ 23%] 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 -[ 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 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: + 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 '< >' -[ 23%] 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 -[ 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 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 +[ 32%] 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 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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 24%] 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 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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 -[ 24%] 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 -[ 24%] 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 -/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], - | ^~~~~~ -[ 24%] 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 -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 24%] Built target mimalloc-obj -[ 25%] 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 -[ 25%] 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 -[ 25%] 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 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+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/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp -[ 26%] 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 -[ 27%] 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 -/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' -[ 27%] Built target edlib -[ 27%] 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 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp -[ 27%] 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 -[ 27%] 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 -[ 27%] 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 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-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 -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend -make[4]: Entering directory 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'/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 29%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -[ 30%] 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/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 -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 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence/sequence_tools.cpp -[ 30%] 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%] 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 -[ 30%] 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 -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] - 73 | #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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); - | ^~~~~~~~~~ -[ 30%] 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 -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] - 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) - | ^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:236:9: note: in expansion of macro 'netwrite' - 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); - | ^~~~~~~~ +[ 32%] 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 +/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/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': -/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] - 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) - | ^~~~~~~~~~~~~~~~~~~ -/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); - | ^~~~~~~~ +[ 32%] 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 +/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 32%] 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 +[ 32%] 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 +[ 33%] 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 +[ 33%] 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 +[ 33%] 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 +[ 33%] 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 +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 +[ 33%] 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 +[ 34%] 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 +[ 34%] 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 +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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 30%] 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 -[ 30%] 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 -[ 30%] 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 -[ 31%] 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 -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o +/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' +[ 34%] Built target sequence +[ 34%] 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 -[ 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 -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: -/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -In file included from /build/reproducible-path/spades-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); - | ^~~~~~~~~~~~~~~~~ -/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/bamtools/api/internal/io/pbgzf/block.c:4: -/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); - | ^~~~~~~~~~~ -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o +[ 34%] 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 -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o +[ 34%] 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 -[ 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 C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -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); - | ^~~~~~~~~~~~~~~~~ -/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/bamtools/api/internal/io/pbgzf/consumer.c:11: -/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/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o cd 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-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 -[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o +[ 36%] 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 -[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o +[ 36%] 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_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 -[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o +[ 37%] 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 +[ 37%] 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 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+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 -[ 33%] 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/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 +[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o +[ 37%] 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_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 -[ 33%] 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 -/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", - | ~~~^ - | | - | long long int - | %ld - 345 | q->mem, q->head, q->tail, q->n, q->length, q->id, q->ordered, q->num_adders, q->num_getters); - | ~~~~~ - | | - | int64_t {aka long int} -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h: At top level: -/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); - | ^~~~~~~~~~~~~~~~~ -/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); - | ^~~~~~~~~~~~~~~ -[ 33%] 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 -[ 34%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -[ 34%] 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/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 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 -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o +[ 37%] 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 -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 - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/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/bamtools/api/internal/io/pbgzf/writer.c:7: -/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_msashuffle.c.o +[ 38%] 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 -[ 36%] 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 -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); - | ^~~~~~~~~~~~~~~~~ -/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/bamtools/api/internal/io/pbgzf/pbgzf.c:13: -/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_msaweight.c.o +[ 38%] 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 -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o +[ 38%] 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 -[ 36%] 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 +[ 38%] 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 +[ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.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/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 '< >' +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 +[ 39%] 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 +[ 39%] 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 +[ 39%] 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 +[ 39%] 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 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; | ^~~~~~~~ +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o /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]': +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 +[ 39%] 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 +/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 36%] 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 /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; @@ -2407,372 +2481,116 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 36%] 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 -[ 36%] 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 -[ 37%] 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 -[ 37%] 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 -[ 38%] 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 -/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' -[ 38%] 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 -[ 38%] Built target format -[ 38%] 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 -[ 38%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_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/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 -[ 38%] 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 -[ 38%] 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 -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); - | ^~~~~~~~~~~~~~~~~ -/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/bamtools/api/internal/io/pbgzf/reader.c:7: -/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); - | ^~~~~~~~~~~ -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.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/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 '< >' +[ 40%] 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 -[ 39%] 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 -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o +[ 40%] 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 C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o +[ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o +[ 41%] 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/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 +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 +[ 41%] 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 +/usr/bin/ar qc libBamTools.a CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o +/usr/bin/ranlib libBamTools.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 41%] Built target BamTools +[ 41%] 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 -[ 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/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 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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/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 -[ 40%] 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 -[ 40%] 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 -[ 40%] 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 -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.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_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_stretchexp.c -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.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 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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_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_tree.c -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.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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'/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/ext/src/samtools 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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 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/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_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.c -[ 43%] 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 -[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.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_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_workqueue.c -[ 43%] 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 -[ 43%] 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 /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_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_wuss.c -[ 44%] 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 -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__ - | ^~~~~~ -[ 44%] 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 -[ 44%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -[ 44%] 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 -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 -[ 45%] 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 -/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)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/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' -[ 45%] Built target graphio -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::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: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +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 +[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.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/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/kstring.c /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 = 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'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; | ^~~~~~~~ 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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/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 -[ 52%] 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 -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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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -MF CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o.d -o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_alidisplay.c -[ 53%] 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 -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 -[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o -[ 54%] 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 && 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CMakeFiles/hmmer.dir/src/p7_gbands.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gbands.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gbands.c -[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.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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CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -/usr/bin/ranlib libBamTools.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 61%] Building C object 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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/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 -[ 61%] 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 -make[4]: 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 -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 -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 61%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -[ 61%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.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/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/kstring.c +[ 43%] 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 +[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.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_aux.c.o -MF CMakeFiles/samtools.dir/bam_aux.c.o.d -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_aux.c -[ 61%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o +[ 43%] 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 +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: +/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +[ 43%] 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 +[ 43%] 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 +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__ + | ^~~~~~ +[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.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.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam.c -[ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o +[ 44%] 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 -[ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o +[ 44%] 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 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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 -isystem /build/reproducible-path/spades-4.0.0+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_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_stretchexp.c +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.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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-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_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_vectorops.c +[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.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 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/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 -/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' -[ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -[ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o +[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.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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-DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-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_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.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); @@ -2798,10 +2616,31 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 63%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.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/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/smoothing_distance_estimation.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/smoothing_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 '< >' +[ 46%] 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 /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_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/easel/esl_wuss.c +[ 46%] Building C object 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 -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_lpileup.c +[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o +[ 47%] 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 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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 -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 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/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/faidx.c -[ 63%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o +[ 47%] 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 +[ 47%] 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 /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_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_sort.c +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.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/sam_header.c.o -MF CMakeFiles/samtools.dir/sam_header.c.o.d -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/sam_header.c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function '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); @@ -2814,7 +2653,6 @@ 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_close': -[ 63%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2844,18 +2682,22 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_sort.c -[ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.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 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CMakeFiles/samtools.dir/sam_header.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/sam_header.c -[ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o +[ 48%] 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 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-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_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/samtools/bam_reheader.c -[ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o +[ 48%] Building C object 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 -[ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o +[ 48%] 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 -[ 65%] Linking CXX static library libllvm-support.a -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 +[ 50%] Linking CXX static library libgraphio.a +cd 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CMakeFiles/easel.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; @@ -2863,6 +2705,8 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/usr/bin/ar qc libeasel.a CMakeFiles/easel.dir/easel.c.o CMakeFiles/easel.dir/esl_alphabet.c.o 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CMakeFiles/easel.dir/esl_msafile2.c.o CMakeFiles/easel.dir/esl_msafile_a2m.c.o CMakeFiles/easel.dir/esl_msafile_afa.c.o CMakeFiles/easel.dir/esl_msafile_clustal.c.o CMakeFiles/easel.dir/esl_msafile_phylip.c.o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o CMakeFiles/easel.dir/esl_msafile_selex.c.o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o CMakeFiles/easel.dir/esl_msashuffle.c.o CMakeFiles/easel.dir/esl_msaweight.c.o CMakeFiles/easel.dir/esl_normal.c.o CMakeFiles/easel.dir/esl_paml.c.o CMakeFiles/easel.dir/esl_random.c.o CMakeFiles/easel.dir/esl_randomseq.c.o CMakeFiles/easel.dir/esl_ratematrix.c.o CMakeFiles/easel.dir/esl_recorder.c.o CMakeFiles/easel.dir/esl_regexp.c.o CMakeFiles/easel.dir/esl_rootfinder.c.o CMakeFiles/easel.dir/esl_scorematrix.c.o CMakeFiles/easel.dir/esl_sq.c.o CMakeFiles/easel.dir/esl_sqio.c.o CMakeFiles/easel.dir/esl_sqio_ascii.c.o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o CMakeFiles/easel.dir/esl_sse.c.o CMakeFiles/easel.dir/esl_ssi.c.o CMakeFiles/easel.dir/esl_stack.c.o CMakeFiles/easel.dir/esl_stats.c.o CMakeFiles/easel.dir/esl_stopwatch.c.o CMakeFiles/easel.dir/esl_stretchexp.c.o CMakeFiles/easel.dir/esl_threads.c.o CMakeFiles/easel.dir/esl_tree.c.o CMakeFiles/easel.dir/esl_vectorops.c.o CMakeFiles/easel.dir/esl_vmx.c.o CMakeFiles/easel.dir/esl_weibull.c.o CMakeFiles/easel.dir/esl_workqueue.c.o CMakeFiles/easel.dir/esl_wuss.c.o +/usr/bin/ranlib libeasel.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; | ^~~~~~~~ @@ -2875,17 +2719,133 @@ /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 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%] Built target llvm-support -[ 65%] 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 -/usr/bin/ar qc libmapping_printer.a CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -/usr/bin/ranlib libmapping_printer.a +[ 50%] Built target easel +make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-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/hmmer /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/hmmer /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/CMakeFiles/hmmer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Built target mapping_printer +make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o +[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o +[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o +[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o +[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o +[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o +[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o +[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o +[ 52%] 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/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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ext/hmmer/CMakeFiles/hmmer.dir/src/generic_msv.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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-I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-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_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_sse.c +[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.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/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 +[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/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 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-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/decoding.c +[ 62%] 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 /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include 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/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; @@ -2893,6 +2853,11 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 63%] 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 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-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/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 +[ 63%] 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 +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o /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; | ^~~~~~~~ @@ -2905,6 +2870,28 @@ /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/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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-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 +[ 63%] 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 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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/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 +[ 65%] 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 +/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' +[ 65%] 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; @@ -2924,13 +2911,29 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 65%] 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 -/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' -[ 65%] Built target samtools +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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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: @@ -2983,9 +2986,35 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +[ 65%] Linking CXX static library libllvm-support.a +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 [ 65%] 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 +/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' +/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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 65%] Built target llvm-support /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' @@ -2997,24 +3026,31 @@ 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 -[ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -[ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.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/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/id_distributor.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_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp -[ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -[ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o +[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o +[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o +[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o +[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o +[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o +[ 67%] 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 -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 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/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.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 +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_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.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_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 -[ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -[ 66%] 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/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 +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 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 -[ 67%] 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 +[ 67%] 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 +[ 67%] 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 +/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' +[ 67%] Built target mapping_printer 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/assembly_graph/graph_support/coverage_uniformity_analyzer.hpp:7, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_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() { | ^ @@ -3037,6 +3073,13 @@ | ^ /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/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 '< >' +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: /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] @@ -3044,8 +3087,7 @@ | ^ /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/coverage_uniformity_analyzer.hpp:7, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp:7: + 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() { | ^ @@ -3054,25 +3096,12 @@ 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 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: + 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 '< >' -/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' -[ 68%] Built target hmmer -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-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' -[ 68%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -[ 68%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -cd /build/reproducible-path/spades-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 -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/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; @@ -3080,13 +3109,6 @@ /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/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 '< >' /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; | ^~~~~~~~ @@ -3108,16 +3130,24 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ +/usr/bin/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' +[ 68%] Built target hmmer +make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-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' +[ 68%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o +[ 68%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o +cd /build/reproducible-path/spades-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 +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/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; | ~~~~^ -[ 68%] 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' 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: @@ -3146,10 +3176,13 @@ /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_; | ^~~~~~~~ +[ 68%] 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' [ 68%] Built target hmmercpp -[ 68%] 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 -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 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]': @@ -3159,6 +3192,9 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 68%] 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 +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 /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' @@ -3227,31 +3263,24 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 8 into object 'tmp' of size 8 580 | value_type tmp(std::forward(args)...); | ^~~ -[ 68%] Linking CXX static library ../../../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 -/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' -[ 68%] Built target gtest -make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-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]: 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=" -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' -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' -[ 68%] 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 -[ 68%] 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 -[ 68%] 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 /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 +/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: @@ -3310,6 +3339,74 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +[ 68%] 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 +[ 68%] 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 +/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' +/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' +[ 68%] Built target ConsensusCore +make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-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=" +[ 68%] Built target gtest +make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-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=" +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 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' +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 ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/build +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build +[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o +[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.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' +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 +[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o +[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o +[ 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/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 +[ 68%] 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/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/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 +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 +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o +[ 69%] 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/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 +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o +[ 69%] 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_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 +[ 70%] 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/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 +[ 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 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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 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 +[ 70%] 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/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 +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 CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o +[ 72%] 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/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/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 +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 +[ 72%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o +[ 72%] 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_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 +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 +[ 72%] 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 /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 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:2151:24: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] @@ -3332,24 +3429,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/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 '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:2151:24: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -3372,169 +3451,109 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 68%] Linking CXX static library ../../../lib/libgtest_main.a +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] + 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/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(debruijn_graph::GraphPack&, const char*)': +/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()); + | ^~~~ +[ 72%] 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 +[ 72%] 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 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_main.dir/link.txt --verbose=1 +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 ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o /usr/bin/ranlib ../../../lib/libgtest_main.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Built target gtest_main -[ 68%] 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 -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 -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Built target teamcity_gtest -[ 68%] 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 -/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' -[ 68%] Built target ConsensusCore -make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-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' -[ 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 -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -[ 69%] 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/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 -[ 69%] 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/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 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp -[ 70%] 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 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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=. 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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 -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/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 -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.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/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: /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 '< >' +[ 72%] Built target gtest_main +/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 +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 72%] Built target teamcity_gtest 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: + 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: /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 '< >' -[ 72%] 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 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: + 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 '< >' 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: + 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/projects/spades/second_phase_setup.cpp:9: + 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 '< >' -/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' -[ 72%] Built target binary_io -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-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=" -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]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.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/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/parser.cpp -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 -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -[ 72%] 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 -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 -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/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -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/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/sam/read.cpp -[ 74%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.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_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.cpp -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/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 -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/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 -[ 74%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.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/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.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/projects/spades/restricted_edges_filling.cpp:11: +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/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(debruijn_graph::GraphPack&, const char*)': -/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()); - | ^~~~ 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/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/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/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/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: + 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/paired_info/is_counter.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.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/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: + 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 '< >' -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/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/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() { | ^ @@ -3542,7 +3561,9 @@ 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/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: + 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() { | ^ @@ -3550,22 +3571,11 @@ 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: + 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/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) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 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 -/usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -/usr/bin/ranlib libassembly_graph.a In file included from /build/reproducible-path/spades-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: @@ -3598,78 +3608,10 @@ /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, | ~~~~~~~^~~~~~~~ -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/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.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/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.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' -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.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/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/paired_info/is_counter.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.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() { - | ^ -[ 75%] 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/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 -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 -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 -/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 -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -[ 75%] 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/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/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 -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 -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 -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 -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -cd 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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/scaffolder2015/scaffold_graph_constructor.cpp.o -[ 79%] 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/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 -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 -[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -[ 79%] 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/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 -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 -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 -[ 80%] 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/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) + | ~~~~~~~^~~ 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] @@ -3678,27 +3620,10 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:458:14: warning: unused variable 'u2' [-Wunused-variable] 458 | bool u2 = UpdateRight(gap, split_orig, split_res); | ^~ -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/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': /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; | ^~~~~~~ -[ 80%] 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/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 '< >' 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]': @@ -3708,12 +3633,6 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 81%] 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 -/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/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) { @@ -3722,6 +3641,43 @@ /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/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/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/paired_info/split_path_constructor.hpp:20: +/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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 72%] 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 +/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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +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: 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_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]': @@ -3737,14 +3693,86 @@ /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/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 '< >' +/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' +[ 72%] 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 /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu 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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 common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build +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' +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/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o +[ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o +[ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o +[ 74%] Building CXX object 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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 && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+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 +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 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common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o +[ 75%] 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/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 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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 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp +[ 76%] 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 && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+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 +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 +[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o +[ 77%] 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/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 +[ 77%] 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/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 +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 +[ 77%] 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 +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o +[ 79%] 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/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 +[ 79%] 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/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 +[ 79%] 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/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 +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 +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_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]': @@ -3773,96 +3801,102 @@ /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/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 '< >' -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 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/paired_info/split_path_constructor.hpp:20: -/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]': +/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' +[ 79%] Built target binary_io +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-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=" +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]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 79%] 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 -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/parser.cpp +[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o +[ 79%] 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/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 +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 +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::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; | ^~~~~~~~ /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/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, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8: +/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.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: + 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 '< >' -/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/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: + 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 '< >' 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: + 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/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: + 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/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_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)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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, @@ -3875,26 +3909,32 @@ | ^ /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/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: + 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() { | ^ +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 '< >' /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/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: + 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: /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/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: + 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() { | ^ @@ -3907,6 +3947,14 @@ | ^ /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/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: @@ -3915,8 +3963,9 @@ | ^ /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/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: + 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() { | ^ @@ -3929,46 +3978,57 @@ 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(path_extend::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/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/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: + 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 '< >' 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: + 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 '< >' -/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/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: + 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() { | ^ @@ -3976,13 +4036,14 @@ 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: + 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 '< >' +[ 80%] 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 -I/build/reproducible-path/spades-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_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.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, @@ -3991,12 +4052,40 @@ 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(path_extend::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_) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +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.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 '< >' +[ 80%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.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/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 +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 '< >' +/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) + | ~~~~~~~~~~~~~~~~^~~~~ 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/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: /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 { @@ -4022,41 +4111,20 @@ /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], | ^~~~~~ +/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(path_extend::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_) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 '< >' -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_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)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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]': @@ -4084,39 +4152,43 @@ /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/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 '< >' -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, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8: -/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()); - | ^~~ +[ 80%] 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 -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp +/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(path_extend::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_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/io/CMakeFiles/input.dir/dataset_support/dataset_readers.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/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp +[ 80%] Building CXX object 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 -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/sam/read.cpp +[ 81%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o +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/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/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 +/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]': @@ -4126,7 +4198,6 @@ /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 = 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; | ^~~~~~~~ @@ -4147,7 +4218,14 @@ | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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 = 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: 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; | ^~~~~~~~ @@ -4161,6 +4239,7 @@ /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:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4173,122 +4252,58 @@ /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/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 '< >' -[ 81%] 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 -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 member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', - inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, - inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, - inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, - inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, - inlined from 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/pair_info_filters.hpp:257:32: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 - 580 | value_type tmp(std::forward(args)...); - | ^~~ -In 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/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>]', - 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:2151:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/streambuf:43, - from /usr/include/c++/14/bits/streambuf_iterator.h:35, - from /usr/include/c++/14/iterator:66, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/boost/iterator.hpp:10, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/boost/iterator/iterator_facade.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/chained_iterator.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/library.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:8: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/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 | 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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/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 | 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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/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' -[ 81%] Built target input /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 = 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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +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/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 '< >' +/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; | ^~~~~~~~ @@ -4307,10 +4322,6 @@ /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/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) - | ~~~~~~~~~~~~~~~~^~~~~ 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: @@ -4351,21 +4362,7 @@ | ^ 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: 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; | ^~~~~~~~ @@ -4412,13 +4409,6 @@ | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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; @@ -4426,34 +4416,6 @@ /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/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: -/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/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]': @@ -4491,14 +4453,12 @@ /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; | ^~~~~~~~ @@ -4511,142 +4471,6 @@ /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/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/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:2151:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/bits/alloc_traits.h:39, - from /usr/include/c++/14/ext/alloc_traits.h:34, - from /usr/include/c++/14/bits/hashtable_policy.h:39, - from /usr/include/c++/14/bits/hashtable.h:35, - from /usr/include/c++/14/bits/unordered_map.h:33, - from /usr/include/c++/14/unordered_map:41, - from /build/reproducible-path/spades-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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/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 | 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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here - 597 | virtual void HandleMerge(const std::vector &old_edges, EdgeId new_edge) override { - | ^~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] - 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In 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:2151:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/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 | 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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function '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 member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', - inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, - inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, - inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, - inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, - inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, - inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, - inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, - inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, - inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:168:43: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 - 580 | value_type tmp(std::forward(args)...); - | ^~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', - inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, - inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, - inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, - inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, - inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, - inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, - inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, - inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, - inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:170:43: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 - 580 | value_type tmp(std::forward(args)...); - | ^~~ -In 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/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 @@ -4792,6 +4616,86 @@ /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 member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', + inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, + inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, + inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, + inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, + inlined from 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/pair_info_filters.hpp:257:32: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 + 580 | value_type tmp(std::forward(args)...); + | ^~~ +In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here + 597 | virtual void HandleMerge(const std::vector &old_edges, EdgeId new_edge) override { + | ^~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] + 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/reproducible-path/spades-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>]', + 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:2151:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/streambuf:43, + from /usr/include/c++/14/bits/streambuf_iterator.h:35, + from /usr/include/c++/14/iterator:66, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/boost/iterator.hpp:10, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/boost/iterator/iterator_facade.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/chained_iterator.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/pipeline/library.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:8: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/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 | 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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/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 | 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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ In file included from /build/reproducible-path/spades-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]': @@ -4801,39 +4705,30 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -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::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/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; | ^~~~~~~~ @@ -4846,18 +4741,67 @@ /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::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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +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:2151:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/bits/alloc_traits.h:39, + from /usr/include/c++/14/ext/alloc_traits.h:34, + from /usr/include/c++/14/bits/hashtable_policy.h:39, + from /usr/include/c++/14/bits/hashtable.h:35, + from /usr/include/c++/14/bits/unordered_map.h:33, + from /usr/include/c++/14/unordered_map:41, + from /build/reproducible-path/spades-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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/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 | 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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ /build/reproducible-path/spades-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; | ^~~~~~~~ @@ -4899,6 +4843,28 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +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:2151:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/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 | 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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ /build/reproducible-path/spades-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; | ^~~~~~~~ @@ -4917,6 +4883,7 @@ /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; | ^~~~~~~~ @@ -4935,6 +4902,16 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +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/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, @@ -4964,6 +4941,61 @@ /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:316:17: warning: 'void operator delete(void*, std::size_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::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', + inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, + inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, + inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, + inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, + inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, + inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, + inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, + inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, + inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:168:43: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 + 580 | value_type tmp(std::forward(args)...); + | ^~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', + inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, + inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, + inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, + inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, + inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, + inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, + inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, + inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, + inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:170:43: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 + 580 | value_type tmp(std::forward(args)...); + | ^~~ +[ 81%] 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 +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 /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; @@ -4989,6 +5021,9 @@ /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 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' /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; | ^~~~~~~~ @@ -5001,6 +5036,7 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 81%] Built target input 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, @@ -5168,7 +5204,7 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -/build/reproducible-path/spades-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::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; | ^~~~~~~~ @@ -5187,7 +5223,7 @@ /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; | ^~~~~~~~ @@ -5244,6 +5280,53 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/build/reproducible-path/spades-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: +/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +/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: @@ -5297,11 +5380,20 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +In file included from /build/reproducible-path/spades-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:2151:24: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + from /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:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: @@ -5341,39 +5433,11 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/reproducible-path/spades-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_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:2151:24: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /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:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: @@ -5420,57 +5484,9 @@ /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: 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: -/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ [ 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' -[ 81%] Built target path_extend -make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.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/pipeline /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/pipeline /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.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/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 -[ 81%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -[ 81%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -[ 81%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -cd /build/reproducible-path/spades-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/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 -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 -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 /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; @@ -5550,6 +5566,26 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/usr/bin/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' +[ 81%] Built target path_extend +make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.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/pipeline /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/pipeline /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.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/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/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/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_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/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 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: @@ -5609,6 +5645,9 @@ /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 { | ~~~~~~~^~~~~~~~ +[ 82%] 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 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]': @@ -5625,12 +5664,14 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/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; | ^~~~~~~~ @@ -5643,32 +5684,27 @@ /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: -/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 82%] 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 +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: +/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ /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' @@ -5783,63 +5819,49 @@ 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/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 projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.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/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.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/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/construction.cpp.o -[ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o +[ 84%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o +[ 84%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o +[ 84%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o +[ 84%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.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 -[ 83%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -[ 83%] 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/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 -[ 83%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.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/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 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/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/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 -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o +[ 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/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 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-DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/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/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 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-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 -[ 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/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 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-DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/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/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 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object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.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/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 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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 -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o +[ 84%] 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/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 +[ 84%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.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/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 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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 +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 [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -[ 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 +[ 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 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-DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/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/hamcluster_1.cpp.o -[ 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 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/ionhammer/hamcluster_1.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 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-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/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 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-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/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/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 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 -/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); @@ -5867,6 +5889,26 @@ /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; + | ~~~~~~~~~~^~ +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] + 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: @@ -5874,6 +5916,15 @@ 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/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 '< >' 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: @@ -5891,21 +5942,6 @@ 93 | static size_t GetDataSize(size_t size) { | ~~~~~~~^~~~ 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: -/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/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] - 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/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] @@ -5936,6 +5972,10 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/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 | } + | ^ 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]': @@ -5945,10 +5985,6 @@ /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/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 | } - | ^ 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: @@ -6027,6 +6063,34 @@ /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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +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: @@ -6177,34 +6241,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ -/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/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:813:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' @@ -6450,185 +6486,178 @@ [ 86%] Built target common_modules make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.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/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend 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[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 -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend +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/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' 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-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend +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-kmercount.dir/DependInfo.cmake "--color=" -make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/depend -make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/depend -make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend +make[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 -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/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[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/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/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' make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.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/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]: 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" 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-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 -make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build -make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build -make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.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/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 -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/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' -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 -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/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=" +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 -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/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' 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/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build 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 -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' 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]: 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 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'/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 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 -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.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/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build +make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build +make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build make[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 projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build -make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.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[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 projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build -[ 86%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -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]: 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[4]: Entering 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]: 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/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -[ 86%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -[ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -[ 86%] 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/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 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-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 -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 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-make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build -[ 86%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -[ 88%] 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/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/corrector && /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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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 -[ 88%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o +make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build +make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/build 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/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/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 -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 -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/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 +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' -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/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.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/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/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 -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 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/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -[ 89%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -[ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -[ 90%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -[ 90%] 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/corrector && /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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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 -[ 90%] 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/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 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-DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/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 -[ 90%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.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/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' make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/build -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 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp -[ 90%] 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/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 make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 90%] 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/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 -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 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-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 -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 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CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o 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 projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-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' +[ 86%] Building CXX object projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o +[ 86%] Building 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projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o +[ 87%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o +[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o +[ 87%] Building CXX object projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o +[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o +[ 87%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o +[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o +[ 87%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o +[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o +[ 96%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o +[ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o +[ 87%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o +[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o +[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o +[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o +[ 96%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o +[ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o +[ 96%] Building CXX object projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o +[ 96%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o +[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o +[ 96%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o +[ 87%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o +[ 87%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o +[ 90%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o +[ 93%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o +[ 96%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o +[ 87%] 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/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_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 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-DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/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/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 -make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build +[ 87%] 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/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 -[ 91%] 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/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 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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 +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 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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/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 -[ 91%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -[ 91%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 91%] 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/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 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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/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 +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 +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 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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 +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 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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 +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 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 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/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp -[ 94%] 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 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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 -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 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/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 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-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 +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 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/usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/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 +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/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 -[ 96%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -[ 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/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 -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 +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 +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 +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 +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 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-DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-4.0.0+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 +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 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/spades/hybrid_aligning.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pipeline.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 '< >' +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 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: @@ -6636,32 +6665,16 @@ 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/pipeline.cpp: In function 'void spades::AddPreliminarySimplificationStages(StageManager&)': -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp:135:19: warning: unused variable 'mode' [-Wunused-variable] - 135 | pipeline_type mode = cfg::get().mode; - | ^~~~ -/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/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 '< >' 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: + 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() { | ^ /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: + 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() { | ^ @@ -6674,34 +6687,23 @@ | ^ /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/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/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() { - | ^ -/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/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 '< >' 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: + 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 '< >' +/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/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]' @@ -6746,7 +6748,15 @@ 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/gmapper/main.cpp:7: + 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] + 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() { | ^ @@ -6760,15 +6770,22 @@ | ^ /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/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/gmapper/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/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: + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pipeline.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 '< >' +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() { | ^ @@ -6780,6 +6797,14 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:357:101: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 357 | for (uint32_t j=0; j::~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/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)) { @@ -6787,6 +6812,17 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp: In function 'void spades::AddPreliminarySimplificationStages(StageManager&)': +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp:135:19: warning: unused variable 'mode' [-Wunused-variable] + 135 | pipeline_type mode = cfg::get().mode; + | ^~~~ +In file included from /build/reproducible-path/spades-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/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, @@ -6803,10 +6839,6 @@ /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/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, @@ -6815,6 +6847,10 @@ 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/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) { + | ^ /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]': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here 197 | debruijn_graph::FastGraphFromSequencesConstructor(k, ext_index).ConstructGraph(g, edge_sequences); @@ -6825,10 +6861,6 @@ /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)); | ^~~~ -/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(); - | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:29: /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] @@ -6841,7 +6873,9 @@ /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; | ^~~~~~~ -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 { @@ -6868,8 +6902,7 @@ 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/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: + 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 { @@ -6895,9 +6928,32 @@ /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/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(); + | ^~~~~~~~~~~~~~~ +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/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/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/projects/cds_subgraphs/main.cpp:13: /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 { @@ -6923,8 +6979,7 @@ /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/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: +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 { @@ -6950,6 +7005,15 @@ /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], | ^~~~~~ +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/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: @@ -6987,6 +7051,27 @@ /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/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]': @@ -6996,6 +7081,17 @@ /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 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/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]': @@ -7005,6 +7101,42 @@ /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/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], + | ^~~~~~ 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]': @@ -7169,93 +7301,6 @@ /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_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()); - | ^~~ -/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]': -/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/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/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], - | ^~~~~~ 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]': @@ -7389,8 +7434,6 @@ /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'; | ^~~~ -[ 96%] 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 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]': @@ -7400,43 +7443,21 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 96%] 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 +[ 96%] Linking CXX executable ../../bin/spades-truseq-scfcorrection [ 96%] 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_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/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+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' [ 96%] Built target spades-corrector-core -[ 96%] 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 -/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' -[ 96%] Built target spades-core /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' [ 96%] Built target spades-truseq-scfcorrection -[ 96%] 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' -[ 96%] Built target spades-convert-bin-to-fasta -[ 96%] Linking CXX executable ../../bin/spades-kmer-estimating -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-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' -[ 96%] Built target spades-kmer-estimating -[ 97%] 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 -/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 +/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-hammer +[ 96%] Built target spades-core /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; | ^~~~~~~~ @@ -7455,8 +7476,30 @@ /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-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 +[ 96%] 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 +[ 97%] 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 +/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' +[ 97%] Built target spades-convert-bin-to-fasta +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: +/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +/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' +[ 97%] Built target spades-hammer +[ 97%] Linking CXX executable ../../bin/spades-kmer-estimating +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-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' +[ 97%] Built target spades-kmer-estimating /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; | ^~~~~~~~ @@ -7484,24 +7527,12 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ /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-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' -[ 98%] Built target spades-read-filter /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; | ^~~~~~~~ @@ -7568,15 +7599,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ /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; | ^~~~~~~~ @@ -7595,8 +7617,6 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 98%] 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 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: /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=] @@ -7606,11 +7626,50 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +[ 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 +[ 98%] Linking CXX executable ../../bin/form_truealignments +[ 98%] 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/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/form_truealignments.dir/link.txt --verbose=1 +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 +/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' +[ 98%] 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 +[ 98%] Built target unitig-coverage +/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' +[ 98%] Built target form_truealignments /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' [ 98%] Built target spades-kmercount -[ 98%] 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-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' +[ 98%] Built target spades-read-filter +[ 98%] 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 +[ 98%] 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 +[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 +/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/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' +[100%] Built target spades-gmapper +[100%] Built target spaligner +/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 /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; | ^~~~~~~~ @@ -7629,6 +7688,14 @@ /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[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 +/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: /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=] @@ -7638,40 +7705,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -/usr/bin/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' -[ 98%] Built target unitig-coverage -[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/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 -[100%] 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/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' -[100%] Built target spaligner -/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 -/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' -[100%] Built target form_truealignments -[100%] 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 -[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 -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 -/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' -[100%] Built target spades-gmapper -/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; | ^~~~~~~~ @@ -7684,6 +7717,9 @@ /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/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' +[100%] Built target cds-mapping-stats 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: /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=] @@ -7720,16 +7756,16 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -[100%] Linking CXX executable ../../bin/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-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' [100%] Built target spades-gbuilder +[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 @@ -7747,125 +7783,125 @@ 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 -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 -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[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' -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[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 -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make[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/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-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 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/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=" +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[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 -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/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=" +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/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[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=" +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/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[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/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=" +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[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/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=" Dependencies file "common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.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". -Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.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/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". Dependencies file "ext/cppformat/CMakeFiles/format.dir/format.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". -Dependencies file "ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.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/googletest/googletest/CMakeFiles/gtest.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/edlib/CMakeFiles/edlib.dir/edlib.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/edlib/CMakeFiles/edlib.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o.d" is newer than depends file "/build/reproducible-path/spades-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/pbgzf/bgzf.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/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". 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Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.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 -f ext/cppformat/CMakeFiles/format.dir/build.make 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]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. +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 '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' -Consolidate compiler generated dependencies of target gtest -[ 4%] Built target paired_info -[ 4%] Built target coverage_model -[ 4%] Built target format -Consolidate compiler generated dependencies of target mimalloc-obj -Consolidate compiler generated dependencies of target edlib -Consolidate compiler generated dependencies of target gqf +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[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]: 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 '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' -make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build -[ 4%] Built target binary_io -[ 45%] Built target llvm-support -[ 45%] Built target BamTools -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build -[ 9%] Built target version -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build make[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' -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/mimalloc/CMakeFiles/mimalloc-obj.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[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]: 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' +[ 11%] Built target paired_info +[ 11%] Built target format +[ 11%] Built target binary_io +[ 11%] Built target coverage_model +[ 11%] Built target gtest +[ 11%] Built target version +[ 11%] Built target edlib +[ 16%] Built target gqf +[ 16%] Built target mimalloc-obj +[ 52%] Built target BamTools +[ 52%] Built target llvm-support make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.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/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[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/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/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=" -[ 47%] Built target gtest -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend +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/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". +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/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/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". 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". +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 "ext/samtools/CMakeFiles/samtools.dir/bam_import.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/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=" Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_index.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 "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 "ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.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_md.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_pileup.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_reheader.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_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 "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 "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". +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 "ext/samtools/CMakeFiles/samtools.dir/faidx.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/kprobaln.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/kstring.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/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". -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 "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". -[ 50%] Built target mimalloc-obj -[ 52%] Built target edlib -[ 52%] Built target gqf -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.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/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=" +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". Consolidate compiler generated dependencies of target teamcity_gtest +Consolidate compiler generated dependencies of target utils +Consolidate compiler generated dependencies of target sequence +Consolidate compiler generated dependencies of target samtools +make[5]: Leaving directory '/build/reproducible-path/spades-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' 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 samtools +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +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' +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 -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.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/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/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". -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". -[ 52%] Built target teamcity_gtest -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". -Consolidate compiler generated dependencies of target sequence -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". -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/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". -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build -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 'common/sequence/CMakeFiles/sequence.dir/build'. +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 -[ 57%] Built target sequence +[ 54%] Built target teamcity_gtest +[ 61%] Built target sequence +[ 64%] Built target samtools +[ 64%] Built target utils make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -Consolidate compiler generated dependencies of 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/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=" -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 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' +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/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/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/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/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". +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/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/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/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/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/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". Dependencies file "common/io/CMakeFiles/input.dir/reads/paired_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". -[ 64%] Built target utils +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/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". -make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend 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' -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/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". +Consolidate compiler generated dependencies of target assembly_graph Consolidate compiler generated dependencies of target input 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 make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.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". -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". 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/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". -[ 69%] Built target input -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 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 input [ 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 @@ -8064,19 +8100,19 @@ 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 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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". 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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/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". @@ -8089,18 +8125,18 @@ Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-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/scaffolder2015/scaffold_graph_visualizer.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". Consolidate compiler generated dependencies of 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/CMakeFiles/modules.dir/build.make 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' +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' 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' -[ 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' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 80%] Built target modules [ 88%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -8149,31 +8185,31 @@ 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' -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/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/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 +[ 92%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o +[ 92%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o +[ 92%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o +[ 92%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o +[ 92%] 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/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/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/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/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 +[ 95%] 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/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/test_utils.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_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 -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_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 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 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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/graphio.cpp.o +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o +[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o +[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/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 +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 +[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/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/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 +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 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 -[ 97%] 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 -[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o [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/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 +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/graph_core_test.cpp:7: @@ -8181,15 +8217,15 @@ 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/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: +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() { | ^ /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/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() { | ^ @@ -8202,13 +8238,13 @@ | ^ /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/test/debruijn/construction_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/construction_test.cpp:7: + 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() { | ^ @@ -8220,6 +8256,14 @@ 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/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 '< >' /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::RawPoint&)': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:24:12: warning: unused variable 'read_count' [-Wunused-variable] 24 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, @@ -8235,14 +8279,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:128:24: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 128 | EdgeId new_id = graph.AddEdge(start_id, fin_id, Graph::EdgeData(tmp), eid, conj_eid); | ^~~~~~ -In file included from /build/reproducible-path/spades-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: -/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/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadPositions(const std::string&, omnigraph::EdgesPositionHandler&)': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:193:13: warning: variable 'read_count' set but not used [-Wunused-but-set-variable] 193 | int read_count = fscanf(file, "%zu\n", &pos_count); @@ -8285,6 +8321,15 @@ 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_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]': @@ -8309,15 +8354,13 @@ /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_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; + | ^~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:115:30: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] + 115 | ends_cfg.penalty_ratio = 0.1; + | ^~~ /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(); @@ -8334,13 +8377,6 @@ /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()); | ^~~ -/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; - | ^~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:115:30: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] - 115 | ends_cfg.penalty_ratio = 0.1; - | ^~~ /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_DijkstraOneEdgeTest_Test::TestBody()': /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:153:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 153 | if (g.int_id(*it) == eid_int){ @@ -8352,6 +8388,49 @@ /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/modules/graph_construction.hpp:13, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:14: +/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]': +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' + 547 | FastGraphFromSequencesConstructor(kmer_size_, origin_).ConstructGraph(graph_, edge_sequences); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' + 59 | g_c.ConstructGraph(params.keep_perfect_loops); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' + 68 | return ConstructGraphUsingExtensionIndex(params, workdir, streams, g); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:77:37: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphWithIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&, EdgeIndex&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' + 77 | KMerFiles kmers = ConstructGraph(params, workdir, streams, g); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:75:28: required from here + 75 | ConstructGraphWithIndex(config::debruijn_config::construction(), workdir, streams, graph, index); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 488 | graph.ereserve(size_t(2.01*sequences.size())); + | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-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/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]': @@ -8398,49 +8477,6 @@ /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/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/modules/graph_construction.hpp:13, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:14: -/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]': -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' - 547 | FastGraphFromSequencesConstructor(kmer_size_, origin_).ConstructGraph(graph_, edge_sequences); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' - 59 | g_c.ConstructGraph(params.keep_perfect_loops); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' - 68 | return ConstructGraphUsingExtensionIndex(params, workdir, streams, g); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:77:37: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphWithIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&, EdgeIndex&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' - 77 | KMerFiles kmers = ConstructGraph(params, workdir, streams, g); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:75:28: required from here - 75 | ConstructGraphWithIndex(config::debruijn_config::construction(), workdir, streams, graph, index); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 488 | graph.ereserve(size_t(2.01*sequences.size())); - | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-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/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]': @@ -8457,80 +8493,60 @@ /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::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/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()); + | ^~~ 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::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::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::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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -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/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()); - | ^~~ -In file included from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13: -/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]': -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' - 547 | FastGraphFromSequencesConstructor(kmer_size_, origin_).ConstructGraph(graph_, edge_sequences); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' - 59 | g_c.ConstructGraph(params.keep_perfect_loops); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' - 68 | return ConstructGraphUsingExtensionIndex(params, workdir, streams, g); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:138:19: required from here - 138 | ConstructGraph(config::debruijn_config::construction(), workdir, streams, g); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 488 | graph.ereserve(size_t(2.01*sequences.size())); - | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-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/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; @@ -8565,6 +8581,26 @@ /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/modules/graph_construction.hpp:13: +/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]': +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' + 547 | FastGraphFromSequencesConstructor(kmer_size_, origin_).ConstructGraph(graph_, edge_sequences); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' + 59 | g_c.ConstructGraph(params.keep_perfect_loops); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' + 68 | return ConstructGraphUsingExtensionIndex(params, workdir, streams, g); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:138:19: required from here + 138 | ConstructGraph(config::debruijn_config::construction(), workdir, streams, g); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 488 | graph.ereserve(size_t(2.01*sequences.size())); + | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-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)); + | ^~~~ /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(); @@ -8605,33 +8641,6 @@ /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:316:17: warning: 'void operator delete(void*, std::size_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: -/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ In file included from /build/reproducible-path/spades-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: @@ -8660,24 +8669,6 @@ /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], | ^~~~~~ -/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/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]': @@ -8744,15 +8735,6 @@ /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); | ^~~ -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: -/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ In file included from /build/reproducible-path/spades-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]' @@ -8764,38 +8746,6 @@ /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ -In file included from /build/reproducible-path/spades-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::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 = 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/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /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(); @@ -8830,18 +8780,16 @@ /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 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: 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; | ^~~~~~~~ @@ -8940,6 +8888,14 @@ /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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +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; @@ -8947,6 +8903,7 @@ /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; | ^~~~~~~~ @@ -8959,7 +8916,21 @@ /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::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 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: +/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ /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; | ^~~~~~~~ @@ -8978,6 +8949,15 @@ /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 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 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: /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=] @@ -9005,63 +8985,55 @@ /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:2151:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence/quality.hpp:18, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/single_read.hpp:11, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.hpp:9, - from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:7: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/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 | 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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/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 | 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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In file included from /build/reproducible-path/spades-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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/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::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; | ^~~~~~~~ @@ -9075,7 +9047,6 @@ /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 = 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; | ^~~~~~~~ @@ -9088,6 +9059,7 @@ /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::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; | ^~~~~~~~ @@ -9125,13 +9097,41 @@ /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 = 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: 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 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: +/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ /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; | ^~~~~~~~ @@ -9144,6 +9144,7 @@ /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::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; | ^~~~~~~~ @@ -9162,6 +9163,60 @@ /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:2151:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/sequence/quality.hpp:18, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/common/io/reads/single_read.hpp:11, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/test_utils.hpp:9, + from /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:7: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/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 | 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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/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 | 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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ /build/reproducible-path/spades-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; @@ -9181,7 +9236,6 @@ /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 = 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; | ^~~~~~~~ @@ -9200,6 +9254,15 @@ /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: +/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ /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; @@ -9281,33 +9344,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/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: -/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 'void omnigraph::PairedVertex::AddOutgoingEdge(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:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, 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:2151:24: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [408]' [-Warray-bounds=] @@ -9352,50 +9388,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In 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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/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 | 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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/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 | 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:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ /build/reproducible-path/spades-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; @@ -9466,6 +9458,50 @@ /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> >, 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:2151:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In 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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/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 | 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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/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 | 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:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ In member function '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: /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=] @@ -9540,156 +9576,156 @@ 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 -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.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/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' -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/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.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/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[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/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/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 -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/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=" +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/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 +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 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/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/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[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]: 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[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/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[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/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' 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 -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build 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=" +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' -make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.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/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]: 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]: 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/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 ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make 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]: 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 -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 '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]: 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]: 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]: 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[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/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 '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 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[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 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/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/googletest/googletest/CMakeFiles/gtest.dir/build.make 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 -[ 2%] Built target format +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/bamtools/api/CMakeFiles/BamTools.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 -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 'common/paired_info/CMakeFiles/paired_info.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' -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]: 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]: 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 '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' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[5]: Entering directory '/build/reproducible-path/spades-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' -[ 4%] Built target gqf [ 7%] Built target version -[ 9%] Built target mimalloc-obj -[ 12%] Built target edlib -[ 12%] Built target coverage_model +[ 7%] Built target format +[ 9%] Built target edlib +[ 12%] Built target gqf +[ 12%] Built target mimalloc-obj +[ 12%] Built target gtest make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.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 common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend -[ 12%] Built target binary_io -[ 12%] Built target gtest 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' -[ 12%] Built target paired_info +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=" +[ 12%] 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/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[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' -[ 31%] Built target BamTools +[ 12%] Built target paired_info +[ 12%] Built target coverage_model 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=" +[ 31%] 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' 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[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 -f ext/llvm/CMakeFiles/llvm-support.dir/build.make 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]: 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 -[ 53%] Built target llvm-support +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make 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 common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.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' 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' -[ 53%] Built target teamcity_gtest -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 -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 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]: 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' -[ 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' -[ 63%] Built target samtools -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -[ 65%] Built target utils +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 +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' +[ 31%] Built target teamcity_gtest +[ 36%] Built target sequence +[ 46%] Built target utils +[ 65%] Built target llvm-support +[ 65%] Built target samtools make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend +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=" 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' -[ 70%] Built target input -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/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' +[ 75%] 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 @@ -9702,13 +9738,13 @@ 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' -make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. +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' 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]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 85%] Built target path_extend -[ 90%] Built target modules +[ 90%] Built target path_extend +[ 82%] Built target modules make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.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/pipeline /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/pipeline /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" @@ -9742,22 +9778,22 @@ 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 -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 -[ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -[ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -[ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -[ 95%] 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/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 -[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_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 +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_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/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/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 +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_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/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 +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/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 +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/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/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 -[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 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, @@ -9966,10 +10002,10 @@ 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 -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 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 -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j40 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 @@ -10059,7 +10095,7 @@ 1: [ RUN ] RtSeq.ShiftLeft 1: [ OK ] RtSeq.ShiftLeft (0 ms) 1: [ RUN ] RtSeq.ShiftLeftThis -1: [ OK ] RtSeq.ShiftLeftThis (0 ms) +1: [ OK ] RtSeq.ShiftLeftThis (1 ms) 1: [ RUN ] RtSeq.ShiftRight 1: [ OK ] RtSeq.ShiftRight (0 ms) 1: [ RUN ] RtSeq.ShiftRightThis @@ -10075,7 +10111,7 @@ 1: [ RUN ] RtSeq.ToSeq 1: [ OK ] RtSeq.ToSeq (0 ms) 1: [ RUN ] RtSeq.FromType -1: [ OK ] RtSeq.FromType (1 ms) +1: [ OK ] RtSeq.FromType (0 ms) 1: [ RUN ] RtSeq.PushBack 1: [ OK ] RtSeq.PushBack (0 ms) 1: [ RUN ] RtSeq.PushBackThis @@ -10135,36 +10171,36 @@ 1: [----------] Global test environment tear-down 1: [==========] 58 tests from 7 test suites ran. (1 ms total) 1: [ PASSED ] 58 tests. -1/2 Test #1: include_test ..................... Passed 0.02 sec +1/2 Test #1: include_test ..................... Passed 0.00 sec 2: Running main() from gtest_main.cpp 2: [==========] Running 98 tests from 10 test suites. 2: [----------] Global test environment set-up. 2: [----------] 6 tests from GraphCore 2: [ RUN ] GraphCore.Empty -2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.006 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.Empty (7 ms) +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.Empty (0 ms) 2: [ RUN ] GraphCore.OneVertex -2: 0:00:00.006 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.006 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneVertex (0 ms) 2: [ RUN ] GraphCore.OneEdge -2: 0:00:00.007 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.007 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneEdge (0 ms) 2: [ RUN ] GraphCore.VertexMethods -2: 0:00:00.007 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.007 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.VertexMethods (0 ms) 2: [ RUN ] GraphCore.SmartIterator -2: 0:00:00.007 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.007 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SmartIterator (0 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge -2: 0:00:00.007 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.007 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SelfRCEdgeMerge (0 ms) -2: [----------] 6 tests from GraphCore (8 ms total) +2: [----------] 6 tests from GraphCore (0 ms total) 2: 2: [----------] 1 test from Histogram 2: [ RUN ] Histogram.StrongWeakPtrBasic @@ -10185,9 +10221,9 @@ 2: [ RUN ] PairedInfo.Prune 2: [ OK ] PairedInfo.Prune (0 ms) 2: [ RUN ] PairedInfo.Neighbours -2: [ OK ] PairedInfo.Neighbours (0 ms) +2: [ OK ] PairedInfo.Neighbours (1 ms) 2: [ RUN ] PairedInfo.DoubledInfo -2: [ OK ] PairedInfo.DoubledInfo (1 ms) +2: [ OK ] PairedInfo.DoubledInfo (0 ms) 2: [ RUN ] PairedInfo.HalfNeighbours 2: [ OK ] PairedInfo.HalfNeighbours (0 ms) 2: [ RUN ] PairedInfo.MoreNeighbours @@ -10197,10 +10233,10 @@ 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry -2: 0:00:00.012 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.016 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] PairedInfo.RandomSymmetry (75 ms) -2: [----------] 13 tests from PairedInfo (77 ms total) +2: 0:00:00.001 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.001 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] PairedInfo.RandomSymmetry (36 ms) +2: [----------] 13 tests from PairedInfo (38 ms total) 2: 2: [----------] 13 tests from OverlapAnalysis 2: [ RUN ] OverlapAnalysis.Trivial @@ -10208,7 +10244,7 @@ 2: [ OK ] OverlapAnalysis.Trivial (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. -2: [ OK ] OverlapAnalysis.Mismatch (1 ms) +2: [ OK ] OverlapAnalysis.Mismatch (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch2 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Mismatch2 (0 ms) @@ -10239,858 +10275,858 @@ 2: [ OK ] OverlapAnalysis.SimpleGap (0 ms) 2: [ RUN ] OverlapAnalysis.UndefinedBehavior 2: [ OK ] OverlapAnalysis.UndefinedBehavior (0 ms) -2: [----------] 13 tests from OverlapAnalysis (2 ms total) +2: [----------] 13 tests from OverlapAnalysis (0 ms total) 2: 2: [----------] 17 tests from Simplification 2: [ RUN ] Simplification.SimpleTipClipperTest -2: 0:00:00.094 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.100 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.111 1M / 9M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp -2: 0:00:00.118 1M / 9M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started -2: 0:00:00.121 1M / 13M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip -2: [ OK ] Simplification.SimpleTipClipperTest (45 ms) +2: 0:00:00.038 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.038 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.039 1M / 9M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp +2: 0:00:00.039 1M / 9M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started +2: 0:00:00.041 1M / 13M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip +2: [ OK ] Simplification.SimpleTipClipperTest (78 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest -2: 0:00:00.134 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.134 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.134 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:00.134 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.137 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.142 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance -2: [ OK ] Simplification.SimpleBulgeRemovalTest (13 ms) +2: 0:00:00.116 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.117 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.117 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:00.117 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.117 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.117 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance +2: [ OK ] Simplification.SimpleBulgeRemovalTest (1 ms) 2: [ RUN ] Simplification.TipobulgeTest -2: 0:00:00.147 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.147 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.147 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:00.147 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:00.148 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:00.148 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance -2: [ OK ] Simplification.TipobulgeTest (2 ms) +2: 0:00:00.117 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.117 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.117 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:00.118 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:00.118 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.118 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance +2: [ OK ] Simplification.TipobulgeTest (1 ms) 2: [ RUN ] Simplification.SimpleECTest -2: 0:00:00.148 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.148 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.148 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.148 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.183 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleECTest (84 ms) +2: 0:00:00.118 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.118 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.118 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.118 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.143 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleECTest (40 ms) 2: [ RUN ] Simplification.SimpleIterECTest -2: 0:00:00.232 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.238 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.241 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.251 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.294 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleIterECTest (111 ms) +2: 0:00:00.159 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.159 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.159 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.159 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.180 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleIterECTest (37 ms) 2: [ RUN ] Simplification.IterECTest -2: 0:00:00.343 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.352 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.358 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.361 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.403 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.IterECTest (96 ms) +2: 0:00:00.196 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.196 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.196 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.196 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.217 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.IterECTest (38 ms) 2: [ RUN ] Simplification.IterUniquePath -2: 0:00:00.440 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.442 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.446 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.452 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.493 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: 0:00:00.495 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: 0:00:00.527 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: [ OK ] Simplification.IterUniquePath (147 ms) +2: 0:00:00.233 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.233 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.233 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.233 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.255 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: 0:00:00.255 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: 0:00:00.262 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: [ OK ] Simplification.IterUniquePath (44 ms) 2: [ RUN ] Simplification.MFUniquePath -2: 0:00:00.587 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.591 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.591 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp -2: 0:00:00.591 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started -2: 0:00:00.614 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path -2: 0:00:00.619 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy -2: [ OK ] Simplification.MFUniquePath (104 ms) +2: 0:00:00.277 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.277 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.277 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp +2: 0:00:00.278 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started +2: 0:00:00.293 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path +2: 0:00:00.294 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy +2: [ OK ] Simplification.MFUniquePath (47 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge -2: 0:00:00.691 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.693 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.702 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:00.710 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.711 1M / 60M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.714 1M / 60M INFO General (simplification_test.cpp : 276) Done -2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (23 ms) +2: 0:00:00.324 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.324 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.324 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:00.324 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.325 1M / 61M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.325 1M / 61M INFO General (simplification_test.cpp : 276) Done +2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (1 ms) 2: [ RUN ] Simplification.ComplexBulge -2: 0:00:00.715 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.715 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.715 1M / 60M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.715 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:00.715 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:00.746 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:00.750 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:00.828 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.919 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: 0:00:00.921 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.980 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:00.987 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: [ OK ] Simplification.ComplexBulge (328 ms) +2: 0:00:00.325 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.325 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.326 1M / 61M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.326 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:00.326 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.345 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:00.346 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:00.373 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.428 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: 0:00:00.428 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.459 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.460 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: [ OK ] Simplification.ComplexBulge (186 ms) 2: [ RUN ] Simplification.BigComplexBulge -2: 0:00:01.042 1M / 62M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.049 1M / 62M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.055 1M / 62M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.061 1M / 62M 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: 0:00:01.071 1M / 62M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:01.224 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge -2: 0:00:01.230 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) -2: 0:00:01.273 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.384 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: 0:00:01.384 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.473 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:01.473 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 (496 ms) +2: 0:00:00.511 1M / 63M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.512 1M / 63M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.512 1M / 63M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.512 1M / 63M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp +2: 0:00:00.512 1M / 63M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:00.761 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge +2: 0:00:00.772 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) +2: 0:00:00.868 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.144 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: 0:00:01.152 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:01.249 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:01.260 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 (889 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover -2: 0:00:01.539 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.544 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.544 1M / 152M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.544 1M / 152M 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: 0:00:01.544 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:01.553 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:01.554 1M / 152M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) -2: 0:00:01.564 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.635 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). -2: 0:00:01.642 2M / 152M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.690 2M / 152M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:01.700 2M / 152M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:01.706 2M / 152M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover (252 ms) +2: 0:00:01.400 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.408 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.416 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:01.432 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp +2: 0:00:01.440 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:01.444 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:01.460 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) +2: 0:00:01.483 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.579 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). +2: 0:00:01.588 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:01.624 2M / 154M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:01.632 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:01.640 2M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover (339 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 -2: 0:00:01.790 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.792 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.802 1M / 152M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.806 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:01.814 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:01.858 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:01.862 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:01.923 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.049 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: 0:00:02.054 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:02.123 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:02.126 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:02.126 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover1 (404 ms) +2: 0:00:01.739 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.748 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.764 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:01.766 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:01.769 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:01.831 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:01.840 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:01.935 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.039 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: 0:00:02.042 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.147 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:02.152 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:02.160 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover1 (516 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 -2: 0:00:02.195 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.204 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.211 1M / 152M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.223 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp -2: 0:00:02.234 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started -2: 0:00:02.247 3M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:02.248 3M / 152M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) -2: 0:00:02.248 3M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.251 3M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). -2: 0:00:02.258 3M / 152M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:02.271 3M / 152M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:02.278 3M / 152M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:02.278 3M / 152M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover2 (101 ms) +2: 0:00:02.255 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.260 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.268 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.276 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp +2: 0:00:02.284 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started +2: 0:00:02.292 3M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:02.300 3M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) +2: 0:00:02.316 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.328 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). +2: 0:00:02.328 3M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.329 3M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:02.329 3M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:02.329 3M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover2 (104 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 -2: 0:00:02.296 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.298 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.298 1M / 152M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.298 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:02.301 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:02.302 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:02.302 1M / 152M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) -2: 0:00:02.302 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.311 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). -2: 0:00:02.311 1M / 152M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:02.312 1M / 152M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:02.312 1M / 152M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:02.312 1M / 152M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover3 (17 ms) +2: 0:00:02.359 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.360 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.360 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.360 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:02.360 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:02.360 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:02.360 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) +2: 0:00:02.360 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.361 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). +2: 0:00:02.361 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.361 1M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:02.362 1M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:02.362 1M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover3 (4 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 -2: 0:00:02.314 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.314 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.314 1M / 152M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.314 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp -2: 0:00:02.323 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started -2: 0:00:02.324 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:02.325 4M / 152M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) -2: 0:00:02.326 4M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.337 4M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). -2: 0:00:02.338 4M / 152M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:02.341 4M / 152M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:02.346 4M / 152M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:02.347 4M / 152M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover4 (56 ms) +2: 0:00:02.363 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.364 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.364 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.364 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp +2: 0:00:02.372 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started +2: 0:00:02.380 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:02.388 4M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) +2: 0:00:02.404 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.419 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). +2: 0:00:02.432 4M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.448 4M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:02.456 4M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:02.464 4M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover4 (155 ms) 2: [ RUN ] Simplification.CompressorTest -2: 0:00:02.369 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.369 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.369 1M / 152M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.369 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp -2: 0:00:02.370 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started -2: 0:00:02.370 2M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: 0:00:02.371 2M / 152M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) -2: 0:00:02.371 2M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.372 2M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). -2: 0:00:02.372 2M / 152M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:02.372 2M / 152M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:02.372 2M / 152M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: [ OK ] Simplification.CompressorTest (4 ms) -2: [----------] 17 tests from Simplification (2285 ms total) +2: 0:00:02.518 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.528 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.536 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.544 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp +2: 0:00:02.552 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started +2: 0:00:02.560 2M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: 0:00:02.568 2M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) +2: 0:00:02.584 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.600 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). +2: 0:00:02.608 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.624 2M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:02.632 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: [ OK ] Simplification.CompressorTest (116 ms) +2: [----------] 17 tests from Simplification (2596 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread -2: 0:00:02.373 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.373 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.373 1M / 152M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:02.373 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.374 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.374 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.374 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.386 1M / 152M INFO General (kmer_splitters.hpp : 131) Used 2 reads -2: 0:00:02.396 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.405 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:02.410 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:02.414 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.414 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.414 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.414 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.425 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. -2: 0:00:02.425 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.428 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. -2: 0:00:02.434 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.443 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). -2: 0:00:02.446 1M / 152M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:02.447 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:02.448 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:02.448 1M / 152M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:02.448 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:02.449 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:02.449 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:02.449 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:02.449 1M / 152M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:02.449 1M / 152M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:02.449 1M / 152M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:02.449 1M / 152M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:02.449 1M / 152M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:02.449 1M / 152M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread (76 ms) +2: 0:00:02.634 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.634 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.634 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:02.652 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.652 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.652 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.652 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.668 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 2 reads +2: 0:00:02.684 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.700 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:02.708 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:02.716 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:02.724 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:02.740 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:02.748 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:02.768 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. +2: 0:00:02.776 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:02.802 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. +2: 0:00:02.808 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.817 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). +2: 0:00:02.824 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:02.833 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:02.840 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:02.848 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:02.856 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:02.872 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:02.888 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:02.904 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:02.912 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:02.920 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:02.936 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:02.944 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:02.952 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:02.960 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread (342 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 -2: 0:00:02.450 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.451 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.454 1M / 152M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:02.454 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.454 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.454 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.454 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.463 1M / 152M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:02.464 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.467 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. -2: 0:00:02.470 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:02.475 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.475 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.475 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.475 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.487 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. -2: 0:00:02.490 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.494 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. -2: 0:00:02.498 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.504 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). -2: 0:00:02.504 1M / 152M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:02.505 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:02.506 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:02.510 1M / 152M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:02.510 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:02.510 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:02.510 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:02.510 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:02.510 1M / 152M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:02.510 1M / 152M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:02.510 1M / 152M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:02.510 1M / 152M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:02.510 1M / 152M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:02.510 1M / 152M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread2 (62 ms) +2: 0:00:02.976 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.984 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.992 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:03.000 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:03.008 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:03.020 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:03.031 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:03.060 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:03.068 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:03.077 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. +2: 0:00:03.084 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:03.092 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:03.098 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:03.120 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:03.134 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:03.157 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. +2: 0:00:03.168 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:03.203 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. +2: 0:00:03.216 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:03.225 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). +2: 0:00:03.232 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:03.241 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:03.254 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:03.274 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:03.278 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:03.303 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:03.321 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:03.348 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:03.364 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:03.376 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:03.400 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:03.412 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:03.420 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:03.432 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread2 (508 ms) 2: [ RUN ] GraphConstruction.SplitThread -2: 0:00:02.511 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.511 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.511 1M / 152M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:02.511 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.511 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.511 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.511 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.520 1M / 152M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:02.526 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.532 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:02.536 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:02.538 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.542 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.546 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.550 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.562 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:02.566 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.569 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:02.574 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.575 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:02.575 1M / 152M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:02.576 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:02.577 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:02.577 1M / 152M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:02.577 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:02.577 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:02.577 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:02.577 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:02.577 1M / 152M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:02.577 1M / 152M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:02.577 1M / 152M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:02.577 1M / 152M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:02.577 1M / 152M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:02.577 1M / 152M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread (67 ms) +2: 0:00:03.484 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:03.492 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:03.500 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:03.516 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:03.526 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:03.547 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:03.558 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:03.582 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:03.586 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:03.592 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:03.598 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:03.608 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:03.619 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:03.632 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:03.643 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:03.664 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:03.672 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:03.682 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:03.690 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:03.698 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:03.714 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.132 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.140 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.159 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.168 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.185 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:04.196 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.204 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.209 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:04.213 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.221 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.225 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.229 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:04.233 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread (758 ms) 2: [ RUN ] GraphConstruction.SplitThread2 -2: 0:00:02.578 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.582 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.583 1M / 152M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:02.583 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.583 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.583 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.583 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.599 1M / 152M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:02.599 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.601 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:02.606 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:02.606 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.606 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.606 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.606 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.614 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:02.614 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.616 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:02.622 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.623 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). -2: 0:00:02.623 1M / 152M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:02.624 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:02.625 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:02.625 1M / 152M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:02.625 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:02.625 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted -2: 0:00:02.625 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:02.625 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:02.625 1M / 152M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create -2: 0:00:02.625 1M / 152M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:02.625 1M / 152M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:02.625 1M / 152M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:02.625 1M / 152M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:02.625 1M / 152M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread2 (48 ms) +2: 0:00:04.242 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.249 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.256 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.264 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.272 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.288 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.296 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.324 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:04.336 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.346 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:04.356 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.364 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.372 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.392 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.405 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.448 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:04.456 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.465 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:04.476 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.489 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). +2: 0:00:04.500 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.620 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.632 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.642 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.652 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.670 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted +2: 0:00:04.676 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.681 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.681 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create +2: 0:00:04.681 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.681 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.681 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.681 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:04.681 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread2 (522 ms) 2: [ RUN ] GraphConstruction.Buldge -2: 0:00:02.626 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.630 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.630 1M / 152M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:02.630 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.630 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.630 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.630 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.638 1M / 152M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:02.638 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.640 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:02.646 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:02.646 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.646 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.646 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.646 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.655 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. -2: 0:00:02.655 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.657 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:02.662 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.664 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:02.664 1M / 152M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:02.666 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:02.670 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:02.671 1M / 152M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:02.671 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:02.671 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted -2: 0:00:02.671 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:02.671 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:02.671 1M / 152M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create -2: 0:00:02.671 1M / 152M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:02.671 1M / 152M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:02.671 1M / 152M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:02.671 1M / 152M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:02.671 1M / 152M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.Buldge (46 ms) +2: 0:00:04.764 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.772 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.780 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.788 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.796 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.810 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.816 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.840 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:04.843 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.858 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:04.872 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.880 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.885 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.885 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.885 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.912 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. +2: 0:00:04.913 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.940 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:04.946 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.964 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:04.972 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.985 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.992 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:05.000 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:05.008 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:05.032 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted +2: 0:00:05.058 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:05.067 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:05.073 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create +2: 0:00:05.080 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:05.088 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:05.096 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:05.104 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:05.112 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.Buldge (364 ms) 2: [ RUN ] GraphConstruction.CondenseSimple -2: 0:00:02.672 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.672 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.672 1M / 152M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:02.672 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.672 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.672 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.673 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.689 1M / 152M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:02.690 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.693 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:02.694 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:02.694 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.695 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.695 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.695 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.707 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:02.709 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.713 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:02.714 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.719 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:02.726 1M / 152M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:02.728 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:02.729 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:02.729 1M / 152M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:02.734 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:02.749 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:02.750 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:02.750 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:02.750 1M / 152M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:02.750 1M / 152M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:02.750 1M / 152M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:02.750 1M / 152M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:02.750 1M / 152M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:02.750 1M / 152M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.CondenseSimple (78 ms) +2: 0:00:05.128 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.136 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.144 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:05.150 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:05.168 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:05.181 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:05.193 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:05.228 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:05.230 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:05.246 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:05.256 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:05.266 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:05.278 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:05.296 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:05.298 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:05.324 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:05.332 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:05.342 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:05.350 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:05.355 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:05.356 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:05.369 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:05.376 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:05.384 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:05.392 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:05.412 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:05.428 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:05.440 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:05.448 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:05.456 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:05.484 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:05.492 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:05.502 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:05.516 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.CondenseSimple (412 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex -2: 0:00:02.751 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.751 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.751 1M / 152M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.751 1M / 152M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:02.751 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.751 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.751 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.751 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.758 1M / 152M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:02.759 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.761 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:02.766 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:02.766 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.766 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.766 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.766 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.773 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:02.774 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.776 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:02.784 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.791 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:02.798 1M / 152M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:02.799 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:02.800 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:02.800 1M / 152M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:02.800 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:02.800 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:02.800 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:02.800 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:02.800 1M / 152M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:02.800 1M / 152M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:02.800 1M / 152M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:02.800 1M / 152M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:02.800 1M / 152M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:02.800 1M / 152M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:02.800 1M / 152M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:02.800 1M / 152M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:02.800 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.800 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:02.801 1M / 152M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerStoringIndex (51 ms) +2: 0:00:05.540 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.548 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.556 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:05.564 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:05.572 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:05.580 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:05.590 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:05.593 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:05.624 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:05.632 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:05.642 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:05.652 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:05.660 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:05.668 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:05.684 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:05.700 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:05.736 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:05.740 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:05.757 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:05.768 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:05.781 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:05.788 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:05.797 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:05.812 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:05.820 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:05.832 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:05.850 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:05.875 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:05.898 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:05.904 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:05.910 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:05.922 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:05.932 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:05.937 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:05.948 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:05.969 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:05.982 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:05.999 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:06.010 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:06.019 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerStoringIndex (500 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex -2: 0:00:02.801 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.801 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.801 1M / 152M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.801 1M / 152M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:02.801 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.801 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.801 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.801 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.809 1M / 152M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:02.809 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.811 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:02.815 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:02.822 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.823 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.823 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.823 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.834 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:02.842 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.849 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:02.855 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.860 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:02.864 1M / 152M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:02.871 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:02.871 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:02.872 1M / 152M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:02.872 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:02.872 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:02.872 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:02.872 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:02.872 1M / 152M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:02.872 1M / 152M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:02.872 1M / 152M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:02.872 1M / 152M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:02.872 1M / 152M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:02.872 1M / 152M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:02.872 1M / 152M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:02.872 1M / 152M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:02.872 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.872 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:02.872 1M / 152M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerFreeIndex (72 ms) +2: 0:00:06.040 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:06.052 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:06.058 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:06.064 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:06.070 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:06.083 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:06.108 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:06.120 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:06.158 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:06.168 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:06.178 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:06.184 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:06.191 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:06.200 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:06.220 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:06.233 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:06.260 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:06.272 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:06.282 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:06.292 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:06.310 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:06.323 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:06.336 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:06.348 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:06.356 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:06.365 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:06.385 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:06.400 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:06.419 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:06.434 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:06.442 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:06.465 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:06.479 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:06.487 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:06.502 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:06.519 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:06.533 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:06.549 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:06.573 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:06.588 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerFreeIndex (566 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo -2: 0:00:02.873 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.878 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.878 1M / 152M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.879 1M / 152M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 -2: 0:00:02.879 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.879 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.879 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.879 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.894 1M / 152M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:02.895 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.897 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. -2: 0:00:02.902 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:02.902 1M / 152M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:02.902 1M / 152M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:02.902 1M / 152M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:02.902 1M / 152M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:02.913 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. -2: 0:00:02.913 1M / 152M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:02.915 1M / 152M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:02.922 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.923 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). -2: 0:00:02.923 1M / 152M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:02.924 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:02.924 1M / 152M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:02.925 1M / 152M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:02.925 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:02.925 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted -2: 0:00:02.925 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:02.925 1M / 152M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:02.925 1M / 152M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create -2: 0:00:02.925 1M / 152M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:02.925 1M / 152M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:02.925 1M / 152M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:02.925 1M / 152M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create -2: 0:00:02.925 1M / 152M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:02.925 1M / 152M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:02.925 1M / 152M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) -2: 0:00:02.925 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.925 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). -2: 0:00:02.925 1M / 152M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:02.925 1M / 152M INFO General (graph_construction.hpp : 93) Filling coverage index -2: 0:00:02.925 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.926 1M / 152M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). -2: 0:00:02.934 1M / 152M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. -2: 0:00:02.934 1M / 152M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM -2: 0:00:02.934 1M / 152M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process -2: 0:00:02.935 1M / 152M INFO General (graph_pack.cpp : 79) Normalizing done -2: 0:00:02.946 10M / 152M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed -2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (87 ms) -2: [----------] 9 tests from GraphConstruction (587 ms total) +2: 0:00:06.606 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:06.620 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:06.630 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:06.644 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 +2: 0:00:06.654 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:06.667 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:06.687 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:06.698 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:06.736 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:06.750 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:06.755 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. +2: 0:00:06.766 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:06.782 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:06.788 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:06.813 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:06.824 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:06.852 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. +2: 0:00:06.860 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:06.873 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:06.884 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:06.898 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). +2: 0:00:06.908 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:06.916 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:06.922 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:06.932 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:06.943 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:06.972 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted +2: 0:00:06.989 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:07.008 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:07.024 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create +2: 0:00:07.032 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:07.052 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:07.064 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:07.072 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create +2: 0:00:07.084 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:07.100 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:07.108 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) +2: 0:00:07.136 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:07.156 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). +2: 0:00:07.164 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:07.188 1M / 154M INFO General (graph_construction.hpp : 93) Filling coverage index +2: 0:00:07.195 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:07.204 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). +2: 0:00:07.220 1M / 154M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. +2: 0:00:07.228 1M / 154M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM +2: 0:00:07.249 1M / 154M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process +2: 0:00:07.289 1M / 154M INFO General (graph_pack.cpp : 79) Normalizing done +2: 0:00:07.317 10M / 154M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed +2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (732 ms) +2: [----------] 9 tests from GraphConstruction (4704 ms total) 2: 2: [----------] 3 tests from Io 2: [ RUN ] Io.Order -2: 0:00:02.960 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.962 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.017 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.018 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] Io.Order (58 ms) +2: 0:00:07.338 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.352 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.471 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.479 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] Io.Order (202 ms) 2: [ RUN ] Io.PairedInfo -2: [ OK ] Io.PairedInfo (5 ms) +2: [ OK ] Io.PairedInfo (10 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (1 ms) -2: [----------] 3 tests from Io (64 ms total) +2: [----------] 3 tests from Io (213 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor -2: 0:00:03.024 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.024 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.024 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.024 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.026 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathConstructor (2 ms) +2: 0:00:07.551 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.556 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.572 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.576 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:07.592 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathConstructor (49 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove -2: 0:00:03.026 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.026 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.026 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.026 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.026 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemove (0 ms) +2: 0:00:07.600 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.612 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.620 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.628 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:07.637 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemove (45 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps -2: 0:00:03.026 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.027 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.027 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.027 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.027 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (1 ms) +2: 0:00:07.645 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.656 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.664 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.677 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:07.685 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (52 ms) 2: [ RUN ] PathExtend.BidirectionalPathEquals -2: 0:00:03.027 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.027 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.027 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.027 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.027 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathEquals (0 ms) +2: 0:00:07.697 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.704 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.716 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.724 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:07.738 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathEquals (48 ms) 2: [ RUN ] PathExtend.BidirectionalPathSubpaths -2: 0:00:03.027 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.027 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.027 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.027 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.028 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathSubpaths (1 ms) +2: 0:00:07.745 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.752 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.760 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.768 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:07.773 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathSubpaths (39 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveConjugate -2: 0:00:03.028 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.028 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.028 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.028 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.028 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (0 ms) +2: 0:00:07.784 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.797 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.804 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.812 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:07.820 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (44 ms) 2: [ RUN ] PathExtend.BidirectionalPathSearch -2: 0:00:03.028 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.028 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.028 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.028 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.029 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathSearch (0 ms) +2: 0:00:07.828 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.835 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.846 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.858 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:07.866 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathSearch (49 ms) 2: [ RUN ] PathExtend.BidirectionalPathLoopDetector -2: 0:00:03.029 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.029 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.029 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.029 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.029 1M / 152M 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 (5 ms total) +2: 0:00:07.877 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.893 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.900 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.919 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:07.927 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathLoopDetector (57 ms) +2: [----------] 8 tests from PathExtend (383 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff -2: 0:00:03.029 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.029 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.029 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.029 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.034 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] OverlapRemoval.BasicNoDiff (5 ms) +2: 0:00:07.934 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.940 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.951 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.957 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:07.968 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] OverlapRemoval.BasicNoDiff (40 ms) 2: [ RUN ] OverlapRemoval.BasicDiff -2: 0:00:03.034 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.034 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.035 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.035 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.035 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] OverlapRemoval.BasicDiff (1 ms) +2: 0:00:07.974 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:07.980 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:07.992 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:07.998 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:08.004 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] OverlapRemoval.BasicDiff (38 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatConjugateEdges -2: 0:00:03.035 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.035 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.035 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:03.035 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:03.035 1M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: 0:00:03.035 1M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) +2: 0:00:08.012 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.021 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.026 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:08.030 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:08.038 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:08.049 1M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (45 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat -2: 0:00:03.036 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.036 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.036 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.036 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.045 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.046 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeat (11 ms) +2: 0:00:08.057 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.065 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.071 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.078 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.098 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.104 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeat (55 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven -2: 0:00:03.046 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.046 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.046 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.046 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.053 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.053 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatUneven (7 ms) +2: 0:00:08.112 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.118 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.124 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.130 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.148 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.156 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatUneven (52 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected -2: 0:00:03.053 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.053 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.054 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.054 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.060 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.060 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.060 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (7 ms) +2: 0:00:08.164 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.170 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.176 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.180 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.193 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.197 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:08.201 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (41 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect -2: 0:00:03.060 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.060 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.060 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.060 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.071 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.074 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (20 ms) +2: 0:00:08.205 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.214 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.218 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.222 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.237 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.244 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (47 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd -2: 0:00:03.080 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.085 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.091 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.098 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.115 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.117 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.122 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEnd (42 ms) +2: 0:00:08.252 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.258 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.264 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.268 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.281 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.285 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:08.289 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEnd (41 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain -2: 0:00:03.122 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.122 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.122 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.122 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.133 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.133 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.138 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (20 ms) +2: 0:00:08.293 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.302 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.306 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.310 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.324 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.332 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:08.339 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (53 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart -2: 0:00:03.142 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.142 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.142 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.142 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.152 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.158 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.162 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStart (28 ms) +2: 0:00:08.346 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.350 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.354 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.360 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.376 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.384 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:08.393 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStart (54 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain -2: 0:00:03.170 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.170 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.170 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.170 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.178 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.182 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.182 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (12 ms) +2: 0:00:08.400 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.408 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.416 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.424 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.439 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.446 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:08.455 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (62 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication -2: 0:00:03.182 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.182 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.182 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.182 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.189 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplication (9 ms) +2: 0:00:08.462 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.466 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.470 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.476 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.493 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplication (38 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual -2: 0:00:03.191 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.191 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.191 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.191 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.198 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (11 ms) +2: 0:00:08.500 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.508 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.516 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.524 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.542 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (48 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff -2: 0:00:03.202 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.202 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.203 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.203 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.212 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiff (10 ms) +2: 0:00:08.548 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.556 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.564 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.572 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.599 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiff (56 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap -2: 0:00:03.212 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.216 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.216 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.216 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.223 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiffGap (14 ms) +2: 0:00:08.604 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.620 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.628 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.632 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.647 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiffGap (48 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 -2: 0:00:03.226 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.226 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.227 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.227 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.233 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (8 ms) +2: 0:00:08.652 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.666 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.673 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.688 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.705 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (63 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 -2: 0:00:03.234 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.238 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.238 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.238 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.246 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (16 ms) +2: 0:00:08.715 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.725 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.737 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.751 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.769 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (66 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen -2: 0:00:03.250 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.254 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.254 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.254 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.262 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.262 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.262 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (12 ms) +2: 0:00:08.781 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.791 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.798 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.809 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.826 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.833 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:08.843 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (70 ms) 2: [ RUN ] OverlapRemoval.Tricky0 -2: 0:00:03.262 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.262 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.262 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.262 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.271 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.275 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.278 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky0 (16 ms) +2: 0:00:08.851 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.866 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.874 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.889 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.908 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.915 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:08.922 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky0 (79 ms) 2: [ RUN ] OverlapRemoval.Tricky1 -2: 0:00:03.278 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.278 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.278 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.278 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.286 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.290 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.290 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky1 (12 ms) +2: 0:00:08.930 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.934 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:08.942 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:08.949 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:08.965 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:08.973 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:08.984 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky1 (61 ms) 2: [ RUN ] OverlapRemoval.Tricky2 -2: 0:00:03.290 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.290 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.290 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.290 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.298 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.302 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.302 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky2 (12 ms) +2: 0:00:08.991 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:08.996 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:09.008 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:09.016 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:09.039 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:09.048 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:09.060 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky2 (77 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen -2: 0:00:03.302 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.302 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.303 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.303 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.311 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.314 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.314 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicMinEdgeLen (12 ms) +2: 0:00:09.068 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:09.084 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:09.092 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:09.100 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:09.119 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:09.128 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:09.144 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicMinEdgeLen (84 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle -2: 0:00:03.314 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.314 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.314 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.314 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.323 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.326 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:03.330 4M / 152M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.OverlapWithMiddle (16 ms) -2: [----------] 23 tests from OverlapRemoval (301 ms total) +2: 0:00:09.152 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:09.160 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:09.169 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:09.176 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:09.193 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:09.202 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:09.220 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.OverlapWithMiddle (74 ms) +2: [----------] 23 tests from OverlapRemoval (1292 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest -2: 0:00:03.331 1M / 152M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 -2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) +2: 0:00:09.226 1M / 154M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 +2: [ OK ] GraphAligner.EdlibSHWFULLTest (10 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero -2: 0:00:03.331 1M / 152M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 -2: 0:00:03.331 1M / 152M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 -2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) +2: 0:00:09.236 1M / 154M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 +2: 0:00:09.240 1M / 154M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 +2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (14 ms) 2: [ RUN ] GraphAligner.TrivialTest -2: 0:00:03.331 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.331 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.331 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:03.331 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:03.340 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:03.358 5M / 152M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm -2: [ OK ] GraphAligner.TrivialTest (946 ms) +2: 0:00:09.250 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:09.260 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:09.264 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:09.268 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:09.278 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:09.296 5M / 154M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm +2: [ OK ] GraphAligner.TrivialTest (1018 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest -2: 0:00:04.276 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.282 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.286 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.294 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.313 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraOneEdgeTest (42 ms) +2: 0:00:10.268 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:10.276 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:10.278 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:10.288 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:10.299 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraOneEdgeTest (34 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest -2: 0:00:04.319 1M / 152M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.330 1M / 152M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.335 1M / 152M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.341 1M / 152M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.358 4M / 152M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraGrowEndsTest (48 ms) -2: [----------] 5 tests from GraphAligner (1036 ms total) +2: 0:00:10.302 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:10.306 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:10.324 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:10.332 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:10.359 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraGrowEndsTest (68 ms) +2: [----------] 5 tests from GraphAligner (1144 ms total) 2: 2: [----------] Global test environment tear-down -2: [==========] 98 tests from 10 test suites ran. (4367 ms total) +2: [==========] 98 tests from 10 test suites ran. (10370 ms total) 2: [ PASSED ] 98 tests. -2/2 Test #2: debruijn_test .................... Passed 4.39 sec +2/2 Test #2: debruijn_test .................... Passed 10.38 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 4.46 sec +Total Test time (real) = 10.39 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 -j42 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 -j40 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 @@ -11112,31 +11148,31 @@ -- 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/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.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/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_2.fq.gz -- 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.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_truspades -- 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/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/A_R2.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/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/TE.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/AT.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/KR.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/KS.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 +-- 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/manual.html -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/README.md -- Installing: /build/reproducible-path/spades-4.0.0+really3.15.5+dfsg/debian/spades/usr/share/spades/truspades_manual.html @@ -11145,27 +11181,27 @@ -- 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/large_genome_mode.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/construction.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/careful_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/simplification.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/moleculo_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/meta_mode.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/rnaviral_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/isolate_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/meta_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/distance_estimation.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/pe_params.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/toy.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/tsa.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/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/rna_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/distance_estimation.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/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 @@ -11195,46 +11231,46 @@ -- 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/check_test_script.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/correction_iteration_script.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/check_test_script.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/postprocessing_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/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_interlaced_reads.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//stages --- 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/spades_stage.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/pipeline.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/correction_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/postprocessing_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/spades_iteration_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/terminating_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/before_start_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/__init__.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/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/error_correction_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//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/break_by_coverage.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/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_postprocessing.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/barcode_extraction.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/break_by_coverage.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/moleculo_postprocessing.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/string_dist_utils.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/__init__.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/parallel_launcher.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/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//executors -- 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_save_yaml.py @@ -11296,12 +11332,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2385081/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2385081/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/1829647 and its subdirectories -I: Current time: Mon Aug 24 03:25:57 -12 2026 -I: pbuilder-time-stamp: 1787585157 +I: removing directory /srv/workspace/pbuilder/2385081 and its subdirectories +I: Current time: Tue Jul 22 23:14:11 +14 2025 +I: pbuilder-time-stamp: 1753175651